91 results on '"P. Bohn"'
Search Results
2. Latent meaning representations in great-ape gestural communication
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Franke, Michael, Bohn, Manuel, and Fröhlich, Marlen
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Other ,Animal cognition ,Animal Communication ,Bayesian modeling ,Computational Modeling ,Field studies - Abstract
Studies of meaning in human and primate communication face, in principle, similar methodological problems. In both cases, meaning is not observable directly, but must be inferred from more indirect sources, such as directly observable behavior. Recent work in probabilistic cognitive modeling of language use has therefore developed methods of inferring latent se- mantic meaning through the lens of a probabilistic model of language use. In this paper, we explore how to adapt such an approach for insightful investigations of primate communication. Towards this end, we develop a suitable probabilistic model of processes that generate communicative behavior by making use of functionally specified latent meaning representations. As a proof of concept, we apply this model to a rich, annotated data set of orangutan communicative dyadic interaction and conclude that explicit probabilistic modeling can provide additional insights for the study of animal communication pertaining to the context-dependent nature of signals and the gradual evolution of human communication systems.
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- 2024
3. Deriving beliefs about children's moral responsibility from capacity beliefs
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Li, Junyu, Hardecker, Susanne, Haun, Daniel Benjamin Moritz, and Bohn, Manuel
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Philosophy ,Psychology ,Action ,Reasoning ,Theory of Mind - Abstract
Adults have rich beliefs about children's development timelines, and they interpret and react to children's behaviors across ages, holding children responsible to some degree. While children's mental capacity and potential could motivate moral agency attribution, a question remains whether a consistent relation exists between the empirical beliefs about children's various capacities and the responsibility attribution to their behaviors that manifest the corresponding capacities. Here, we tested 361 adults (UK, US) on their folk psychology and moral beliefs about different ages with vignettes that reflect agential control in various domains (motor control, inhibitory control, theory of mind, planning, moral evaluation) combined with several variants of scenarios. We characterized the relation between adults' expectations and responsibility attribution with mixed models. We found that this moral reasoning varies for targets of different ages and the amount of responsibility is mostly determined by age. We suggest an alternative mechanism between capacity- and moral beliefs.
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- 2024
4. High-throughput optofluidic screening of single B cells identifies novel cross-reactive antibodies as inhibitors of uPAR with antibody-dependent effector functions
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Lourenço, André Luiz, Chuo, Shih-Wei, Bohn, Markus F, Hann, Byron, Khan, Shireen, Yevalekar, Neha, Patel, Nitin, Yang, Teddy, Xu, Lina, Lv, Dandan, Drakas, Robert, Lively, Sarah, and Craik, Charles S
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Women's Health ,Breast Cancer ,Immunotherapy ,Immunization ,Cancer ,Biotechnology ,5.1 Pharmaceuticals ,Humans ,Animals ,Mice ,Receptors ,Urokinase Plasminogen Activator ,Leukocytes ,Mononuclear ,Antibodies ,Signal Transduction ,B-Lymphocytes ,Antibody-dependent cellular cytotoxicity ,cancer therapeutics ,cross-reactive antibody ,single B-cell screening ,Urokinase-type plasminogen activator receptor ,Pharmacology and Pharmaceutical Sciences ,Public Health and Health Services ,Pharmacology and pharmaceutical sciences - Abstract
The urokinase-type plasminogen activator receptor (uPAR) is an essential regulator for cell signaling in tumor cell proliferation, adhesion, and metastasis. The ubiquitous nature of uPAR in many aggressive cancer types makes uPAR an attractive target for immunotherapy. Here, we present a rapid and successful workflow for developing cross-reactive anti-uPAR recombinant antibodies (rAbs) using high-throughput optofluidic screening of single B-cells from human uPAR-immunized mice. A total of 80 human and cynomolgus uPAR cross-reactive plasma cells were identified, and selected mouse VH/VL domains were linked to the trastuzumab (Herceptin®) constant domains for the expression of mouse-human chimeric antibodies. The resulting rAbs were characterized by their tumor-cell recognition, binding activity, and cell adhesion inhibition on triple-negative breast cancer cells. In addition, the rAbs were shown to enact antibody-dependent cellular cytotoxicity (ADCC) in the presence of either human natural killer cells or peripheral blood mononuclear cells, and were evaluated for the potential use of uPAR-targeting antibody-drug conjugates (ADCs). Three lead antibodies (11857, 8163, and 3159) were evaluated for their therapeutic efficacy in vivo and were shown to suppress tumor growth. Finally, the binding epitopes of the lead antibodies were characterized, providing information on their unique binding modes to uPAR. Altogether, the strategy identified unique cross-reactive antibodies with ADCC, ADC, and functional inhibitory effects by targeting cell-surface uPAR, that can be tested in safety studies and serve as potential immunotherapeutics.
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- 2023
5. A synthesis of pathways linking diet, metabolic risk and cardiovascular disease: a framework to guide further research and approaches to evidence-based practice.
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Lima do Vale, Marjorie Rafaela, Buckner, Luke, Mitrofan, Claudia Gabriela, Tramontt, Claudia Raulino, Kargbo, Sento Kai, Khalid, Ali, Ashraf, Sammyia, Mouti, Saad, Dai, Xiaowu, Unwin, David, Bohn, Jeffrey, Goldberg, Lisa, Golubic, Rajna, and Ray, Sumantra
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Biomedical and Clinical Sciences ,Nutrition and Dietetics ,Nutrition ,Prevention ,Heart Disease ,Cardiovascular ,2.3 Psychological ,social and economic factors ,Aetiology ,Generic health relevance ,Good Health and Well Being ,Humans ,Cardiovascular Diseases ,Diet ,Risk Factors ,Nutritional Status ,Evidence-Based Practice ,Causality ,Cardiovascular disease ,Review ,Risk factors ,Nutritional status ,Biological Sciences ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Nutrition & Dietetics ,Nutrition and dietetics - Abstract
Cardiovascular disease (CVD) is the most common non-communicable disease occurring globally. Although previous literature has provided useful insights into the important role that diet plays in CVD prevention and treatment, understanding the causal role of diets is a difficult task considering inherent and introduced weaknesses of observational (e.g. not properly addressing confounders and mediators) and experimental research designs (e.g. not appropriate or well designed). In this narrative review, we organised current evidence linking diet, as well as conventional and emerging physiological risk factors, with CVD risk, incidence and mortality in a series of diagrams. The diagrams presented can aid causal inference studies as they provide a visual representation of the types of studies underlying the associations between potential risk markers/factors for CVD. This may facilitate the selection of variables to be considered and the creation of analytical models. Evidence depicted in the diagrams was systematically collected from studies included in the British Nutrition Task Force report on diet and CVD and database searches, including Medline and Embase. Although several markers and disorders linked to conventional and emerging risk factors for CVD were identified, the causal link between many remains unknown. There is a need to address the multifactorial nature of CVD and the complex interplay between conventional and emerging risk factors with natural and built environments, while bringing the life course into the spotlight.
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- 2023
6. Energy Services Interface: Requirements Document
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Brown, Rich, Khandekar, Aditya, Liu, JingJing, Nordman, Bruce, Kolln, Jaime, Widergren, Steve, Narang, David, Bohn, Ted, and Xue, Yaosuo
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This energy services interface (ESI) requirements document represents a process step in the path for creating an ESI specification, which will describe the technical characteristics of an ESI. This document outlines the concepts that need to be covered in the ESI specification, such as principal functions of the ESI, grid services communicated through the ESI, and the ESI lifecycle. It provides context for the Department of Energy’s (DOE’s) Grid Modernization Laboratory Consortium (GMLC) to engage industry participants in the development of the ESI specification. To do this, it describes the desired contents of the ESI specification and provides examples of the type of material that needs to be included in it.The purpose of the ESI specification is to define the requirements that are to be addressed in information and communications technology (ICT) interface standards for enabling the integration of a facility containing responsive distributed energy resources (DER facility) to an electric system consistent with the fundamental ESI principles. In this context, a DER facility may consist of a single DER with a communicating controller or may be as complex as a microgrid campus with several buildings and many DERs. The ESI specification is not a technical interface standard, but the requirements in the specification can be used to check that existing, augmented, or new interface standards meet the interoperability requirements of the ESI concept, which is explained further in this document. In this way, the ESI specification can be used to guide standards advancement work in multiple standards development organizations.To explain the scope of the ESI specification, this ESI requirements document provides examples of situations (or illustrative applications) for using an ESI to coordinate DER flexibility for grid operations. These examples originate from foundational work for describing common grid-DER service agreements that are anticipated to be supported using this interface.
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- 2023
7. Shape from spectra
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Carmon, Nimrod, Berk, Alexander, Bohn, Niklas, Brodrick, Phillip G, Dozier, Jeff, Johnson, Margaret, Miller, Charles E, Thompson, David R, Turmon, Michael, Bachmann, Charles M, Green, Robert O, Eckert, Regina, Liggett, Elliott, Nguyen, Hai, Ochoa, Francisco, Okin, Gregory S, Samuels, Rory, Schimel, David, Song, Joon Jin, and Susiluoto, Jouni
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Earth Sciences ,Bioengineering ,Topography ,Atmospheric correction ,Topographic correction ,Reflectance retrievals ,Imaging spectroscopy ,Surface biology and geology ,Orbital imaging spectroscopy ,Physical Geography and Environmental Geoscience ,Geomatic Engineering ,Geological & Geomatics Engineering ,Earth sciences - Published
- 2023
8. A Resampling Approach for Causal Inference on Novel Two-Point Time-Series with Application to Identify Risk Factors for Type-2 Diabetes and Cardiovascular Disease
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Dai, Xiaowu, Mouti, Saad, do Vale, Marjorie Lima, Ray, Sumantra, Bohn, Jeffrey, and Goldberg, Lisa
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Resampling ,Matching method ,Causal inference ,Two-point time-series ,Synthetic control ,Type-2 diabetes ,Cardiovascular disease ,Bioinformatics and computational biology ,Statistics - Published
- 2023
9. A Resampling Approach for Causal Inference on Novel Two-Point Time-Series with Application to Identify Risk Factors for Type-2 Diabetes and Cardiovascular Disease
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Dai, Xiaowu, Mouti, Saad, Vale, Marjorie Lima do, Ray, Sumantra, Bohn, Jeffrey, and Goldberg, Lisa
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Mathematical Sciences ,Biological Sciences ,Bioinformatics and Computational Biology ,Statistics ,Nutrition ,Diabetes ,Cardiovascular ,Prevention ,Heart Disease ,Obesity ,Management of diseases and conditions ,7.1 Individual care needs ,Metabolic and endocrine ,Good Health and Well Being ,Bioinformatics and computational biology - Abstract
Two-point time-series data, characterized by baseline and follow-up observations, are frequently encountered in health research. We study a novel two-point time-series structure without a control group, which is driven by an observational routine clinical dataset collected to monitor key risk markers of type-2 diabetes (T2D) and cardiovascular disease (CVD). We propose a resampling approach called “I-Rand” for independently sampling one of the two-time points for each individual and making inferences on the estimated causal effects based on matching methods. The proposed method is illustrated with data from a service-based dietary intervention to promote a low-carbohydrate diet (LCD), designed to impact risk of T2D and CVD. Baseline data contain a pre-intervention health record of study participants, and health data after LCD intervention are recorded at the follow-up visit, providing a two-point time-series pattern without a parallel control group. Using this approach we find that obesity is a significant risk factor of T2D and CVD, and an LCD approach can significantly mitigate the risks of T2D and CVD. We provide code that implements our method.
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- 2023
10. State of Common Grid Services Definitions
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Liu, Jingjing, Widergren, Steve, Kolln, Jaime, Bohn, Ted, Xue, Sonny, and Brown, Richard
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This document is prepared as part of the Department of Energy’s Grid Modernization Laboratory Consortium (GMLC) 2.5.2 project, whose goal is to develop and socialize a common set of grid service definitions relevant to grid-related interactions with distributed energy resources (DER: responsive generation, storage, and loads), and to advance the concept and requirements of the Energy Services Interface (ESI) to the point of launching related interface standards and guides that can be implemented in communication protocols and business process definitions. The notion of “grid services” is integral to the definition of an ESI because a key principle of the ESI is that it permits coordination between grid operators and DER facilities in a way that is service-oriented, with an understanding of performance expectations. This document reviews the current state of grid service definitions, including those actively used in the market today as well as new services that have been proposed for future implementation. The document describes grid services used in transmission as well as distribution systems. In defining grid services, this document also distinguishes between two fundamental concepts: an “operational objective” and a “grid service,” which describes a generator’s or customer’s expected physical performance in delivering power to or consuming power from the grid.
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- 2022
11. GOALS-JWST: Resolving the Circumnuclear Gas Dynamics in NGC 7469 in the Mid-infrared
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Vivian, U, Lai, Thomas, Bianchin, Marina, Remigio, Raymond P, Armus, Lee, Larson, Kirsten L, Díaz-Santos, Tanio, Evans, Aaron, Stierwalt, Sabrina, Law, David R, Malkan, Matthew A, Linden, Sean, Song, Yiqing, van der Werf, Paul P, Gao, Tianmu, Privon, George C, Medling, Anne M, Barcos-Muñoz, Loreto, Hayward, Christopher C, Inami, Hanae, Rich, Jeff, Aalto, Susanne, Appleton, Philip, Bohn, Thomas, Böker, Torsten, Brown, Michael JI, Charmandaris, Vassilis, Finnerty, Luke, Howell, Justin, Iwasawa, Kazushi, Kemper, Francisca, Marshall, Jason, Mazzarella, Joseph M, McKinney, Jed, Muller-Sanchez, Francisco, Murphy, Eric J, Sanders, David, and Surace, Jason
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Astronomical and Space Sciences ,Astronomy & Astrophysics - Abstract
The nearby, luminous infrared galaxy NGC 7469 hosts a Seyfert nucleus with a circumnuclear star-forming ring and is thus the ideal local laboratory for investigating the starburst-AGN (active galactic nucleus) connection in detail. We present integral-field observations of the central 1.3 kpc region in NGC 7469 obtained with the JWST Mid-InfraRed Instrument. Molecular and ionized gas distributions and kinematics at a resolution of ∼100 pc over the 4.9-7.6 μm region are examined to study the gas dynamics influenced by the central AGN. The low-ionization [Fe ii] λ5.34 μm and [Ar ii] λ6.99 μm lines are bright on the nucleus and in the starburst ring, as opposed to H2 S(5) λ6.91 μm, which is strongly peaked at the center and surrounding ISM. The high-ionization [Mg v] line is resolved and shows a broad, blueshifted component associated with the outflow. It has a nearly face-on geometry that is strongly peaked on the nucleus, where it reaches a maximum velocity of −650 km s−1, and extends about 400 pc to the east. Regions of enhanced velocity dispersion in H2 and [Fe ii] ∼ 180 pc from the AGN that also show high L(H2)/L(PAH) and L([Fe ii])/L(Pfα) ratios to the W and N of the nucleus pinpoint regions where the ionized outflow is depositing energy, via shocks, into the dense interstellar medium between the nucleus and the starburst ring. These resolved mid-infrared observations of the nuclear gas dynamics demonstrate the power of JWST and its high-sensitivity integral-field spectroscopic capability to resolve feedback processes around supermassive black holes in the dusty cores of nearby luminous infrared galaxies.
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- 2022
12. Incidence and Prevalence of Coronavirus Disease 2019 Within a Healthcare Worker Cohort During the First Year of the Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic
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Doernberg, Sarah B, Holubar, Marisa, Jain, Vivek, Weng, Yingjie, Lu, Di, Bollyky, Jenna B, Sample, Hannah, Huang, Beatrice, Craik, Charles S, Desai, Manisha, Rutherford, George W, Maldonado, Yvonne, Bhargava, Parul, Bohn, Markus, Chao, Jessica, Ghahremani, Jacob, Glidden, David, Gonzales, Ralph, Jaladanki, Sravya, Julien, Aida, Lowenstein, Daniel, Miller, Steve, Mustoe, Audrey, Paoletti, Marcus, Villa, Rodolfo, Wan, Emerald, Williams, Aimee, Brown, Lillian, Chuang, Jessica, Marquez, Carina, Padda, Guntas, Rubio, Luis, Valdivieso, Daisy, Abad, Rosebay, Bet, Anthony, Bollyky, Jenna, Fung, Jeffrey, Graber, Anna, Holderman, Cole, Kelley, Hannah, Kempema, Amanda, Kong, Christina, Leung, Christopher, Lohmann, Joseph, Minor, Lloyd, Orozco, Lorena, Pinsky, Benjamin A, Saxeena, Jamie, Sklar, Matthew, Tang, Hilary, Wiese, Jasmine, Crawford, Emily, and DeRisi, Joe
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Lung ,Emerging Infectious Diseases ,Clinical Research ,Biodefense ,Vaccine Related ,Prevention ,Infectious Diseases ,2.1 Biological and endogenous factors ,2.2 Factors relating to the physical environment ,2.4 Surveillance and distribution ,Aetiology ,Infection ,Good Health and Well Being ,Humans ,SARS-CoV-2 ,Pandemics ,COVID-19 ,Incidence ,Prevalence ,Longitudinal Studies ,Health Personnel ,Cohort Studies ,healthcare worker ,healthcare personnel ,CHART Study Consortium ,Biological Sciences ,Medical and Health Sciences ,Microbiology - Abstract
BackgroundPreventing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2_ infections in healthcare workers (HCWs) is critical for healthcare delivery. We aimed to estimate and characterize the prevalence and incidence of coronavirus disease 2019 (COVID-19) in a US HCW cohort and to identify risk factors associated with infection.MethodsWe conducted a longitudinal cohort study of HCWs at 3 Bay Area medical centers using serial surveys and SARS-CoV-2 viral and orthogonal serological testing, including measurement of neutralizing antibodies. We estimated baseline prevalence and cumulative incidence of COVID-19. We performed multivariable Cox proportional hazards models to estimate associations of baseline factors with incident infections and evaluated the impact of time-varying exposures on time to COVID-19 using marginal structural models.ResultsA total of 2435 HCWs contributed 768 person-years of follow-up time. We identified 21 of 2435 individuals with prevalent infection, resulting in a baseline prevalence of 0.86% (95% confidence interval [CI], .53%-1.32%). We identified 70 of 2414 incident infections (2.9%), yielding a cumulative incidence rate of 9.11 cases per 100 person-years (95% CI, 7.11-11.52). Community contact with a known COVID-19 case was most strongly correlated with increased hazard for infection (hazard ratio, 8.1 [95% CI, 3.8-17.5]). High-risk work-related exposures (ie, breach in protective measures) drove an association between work exposure and infection (hazard ratio, 2.5 [95% CI, 1.3-4.8). More cases were identified in HCWs when community case rates were high.ConclusionsWe observed modest COVID-19 incidence despite consistent exposure at work. Community contact was strongly associated with infections, but contact at work was not unless accompanied by high-risk exposure.
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- 2022
13. A covalent inhibitor of K-Ras(G12C) induces MHC class I presentation of haptenated peptide neoepitopes targetable by immunotherapy
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Zhang, Ziyang, Rohweder, Peter J, Ongpipattanakul, Chayanid, Basu, Koli, Bohn, Markus-Frederik, Dugan, Eli J, Steri, Veronica, Hann, Byron, Shokat, Kevan M, and Craik, Charles S
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Biotechnology ,Immunotherapy ,Immunization ,Vaccine Related ,Cancer ,5.1 Pharmaceuticals ,Antibodies ,Antineoplastic Agents ,Histocompatibility Antigens Class I ,Humans ,Immunologic Factors ,Neoplasms ,Peptides ,Proto-Oncogene Proteins p21(ras) ,ARS1620 ,KRas ,MHC-I ,antibody ,cancer ,covalent inhibitors ,drug resistance ,immunotherapy ,Neurosciences ,Oncology & Carcinogenesis ,Biochemistry and cell biology ,Oncology and carcinogenesis - Abstract
Immunotargeting of tumor-specific antigens is a powerful therapeutic strategy. Immunotherapies directed at MHC-I complexes have expanded the scope of antigens and enabled the direct targeting of intracellular oncoproteins at the cell surface. We asked whether covalent drugs that alkylate mutated residues on oncoproteins could act as haptens to generate unique MHC-I-restricted neoantigens. Here, we report that KRAS G12C mutant cells treated with the covalent inhibitor ARS1620 present ARS1620-modified peptides in MHC-I complexes. Using ARS1620-specific antibodies identified by phage display, we show that these haptenated MHC-I complexes can serve as tumor-specific neoantigens and that a bispecific T cell engager construct based on a hapten-specific antibody elicits a cytotoxic T cell response against KRAS G12C cells, including those resistant to direct KRAS G12C inhibition. With multiple K-RAS G12C inhibitors in clinical use or undergoing clinical trials, our results present a strategy to enhance their efficacy and overcome the rapidly arising tumor resistance.
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- 2022
14. Diagnostic accuracy of [18F]PSMA-1007 PET/CT in biochemical recurrence of prostate cancer.
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Bohn, Karl, Rominger, Axel, Afshar-Oromieh, Ali, Alberts, Ian, and Mingels, Clemens
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Biochemical recurrence ,PET/CT ,PSMA ,Positron emission tomography ,Prostate cancer ,Prostate-specific membrane antigen ,Gallium Radioisotopes ,Humans ,Male ,Niacinamide ,Oligopeptides ,Positron Emission Tomography Computed Tomography ,Prostate-Specific Antigen ,Prostatic Neoplasms ,Retrospective Studies ,Tomography ,X-Ray Computed - Abstract
AIM: Despite increasing use for the detection of biochemically recurrent prostate cancer (rPC), the diagnostic accuracy of positron emission tomography/computed tomography (PET/CT) with [18F]PSMA-1007 remains only partially investigated. The aim of this study was to determine the sensitivity (SE), specificity (SP), positive predictive value (PPV), and negative predictive value (NPV) for PC-local recurrence and metastases on a per region basis. MATERIALS AND METHODS: One hundred seventy-seven consecutive patients undergoing [18F]PSMA-1007 PET/CT for rPC were retrospectively analysed. Six body regions were defined: prostate fossa, pelvic lymph nodes (LN), retroperitoneal LN, supradiaphragmatic LN, bones, and soft tissue. A region was counted positive if at least one PSMA-positive lesion suspicious for PC was observed. Confirmation of a true-positive PSMA-avid lesion was defined as positive by histopathology, fall in serum prostate-specific antigen (PSA) (> 50%) after targeted therapy or confirmatory further CT, MRI, PET/CT, or bone scan imaging. Regions where additional imaging was able to confirm the absence of suspicious PC lesions or regions outside exclusively targeted RT with serum PSA decline (> 50%) were counted as true-negative regions. SE, SP, PPV, and NPV were calculated for all six regions. RESULTS: The overall PET-positivity rate was 91%. Conclusive follow-up for affirmation or refutation of a PSMA-positive lesion was available for 81/152 patients on a per region basis. In this subgroup, overall sensitivity, specificity, PPV, and NPV were 95% (CI: 0.90-0.98), 89% (CI: 0.83-0.93), 86% (0.80-0.90), and 96% (CI: 0.92-0.98), respectively. On a per region basis, PPV was 97% (CI: 0.83-0.99) for local recurrence, 93% (CI: 0.78-0.98) for pelvic LN, 87% (CI: 0.62-0.96) for retroperitoneal LN, 82% (CI: 0.52-0.95) for supradiaphragmatic LN, and 79% (0.65-0.89) for bone lesions. The number of solid organ metastases (n = 6) was too small for an accurate statistical analysis. CONCLUSION: The known high PET-positivity rate of [18F]PSMA-1007 PET/CT in rPC was confirmed, with corresponding high (> 90%) sensitivity and NPV on a per region basis. However, overall PPV was limited (86%), particularly for bone lesions (79%), which are a potential diagnostic weaknesses when using this tracer.
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- 2022
15. Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS
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Goh, Charlene E, Bohn, Bruno, Marotz, Clarisse, Molinsky, Rebecca, Roy, Sumith, Paster, Bruce J, Chen, Ching‐Yuan, Rosenbaum, Michael, Yuzefpolskaya, Melana, Colombo, Paolo C, Desvarieux, Moïse, Papapanou, Panos N, Jacobs, David R, Knight, Rob, and Demmer, Ryan T
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Dental/Oral and Craniofacial Disease ,Genetics ,Human Genome ,Clinical Research ,Infection ,Adult ,Bacteria ,Cardiovascular Diseases ,Female ,Humans ,Male ,Microbiota ,Nitrates ,Nitric Oxide ,Nitrites ,Nitrogen ,Nitrogen Dioxide ,RNA ,Ribosomal ,16S ,16S rNA sequencing ,blood pressure ,epidemiology ,insulin resistance ,metagenomics ,nitric oxide ,oral microbiome ,Cardiorespiratory Medicine and Haematology - Abstract
Background The enterosalivary nitrate-nitrite-nitric oxide (NO3-NO2-NO) pathway generates NO following oral microbiota-mediated production of salivary nitrite, potentially linking the oral microbiota to reduced cardiometabolic risk. Nitrite depletion by oral bacteria may also be important for determining the net nitrite available systemically. We examine if higher abundance of oral microbial genes favoring increased oral nitrite generation and decreased nitrite depletion is associated with a better cardiometabolic profile cross-sectionally. Methods and Results This study includes 764 adults (mean [SD] age 32 [9] years, 71% women) enrolled in ORIGINS (Oral Infections, Glucose Intolerance, and Insulin Resistance Study). Microbial DNA from subgingival dental plaques underwent 16S rRNA gene sequencing; PICRUSt2 was used to estimate functional gene profiles. To represent the different components and pathways of nitrogen metabolism in bacteria, predicted gene abundances were operationalized to create summary scores by (1) bacterial nitrogen metabolic pathway or (2) biochemical product (NO2, NO, or ammonia [NH3]) formed by the action of the bacterial reductases encoded. Finally, nitrite generation-to-depletion ratios of gene abundances were created from the above summary scores. A composite cardiometabolic Z score was created from cardiometabolic risk variables, with higher scores associated with worse cardiometabolic health. We performed multivariable linear regression analysis with cardiometabolic Z score as the outcome and the gene abundance summary scores and ratios as predictor variables, adjusting for sex, age, race, and ethnicity in the simple adjusted model. A 1 SD higher NO versus NH3 summary ratio was inversely associated with a -0.10 (false discovery rate q=0.003) lower composite cardiometabolic Z score in simple adjusted models. Higher NH3 summary score (suggestive of nitrite depletion) was associated with higher cardiometabolic risk, with a 0.06 (false discovery rate q=0.04) higher composite cardiometabolic Z score. Conclusions Increased net capacity for nitrite generation versus depletion by oral bacteria, assessed through a metagenome estimation approach, is associated with lower levels of cardiometabolic risk.
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- 2022
16. How Risky Are Risk Factors? An Analysis of Prenatal Risk Factors in Patients Participating in the Congenital Upper Limb Differences Registry
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Schaeffer, Tyler, Canizares, Maria F, Wall, Lindley B, Bohn, Deborah, Steinman, Suzanne, Samora, Julie, Manske, Mary Claire, Hutchinson, Douglas T, Shah, Apurva S, Bauer, Andrea S, Group, CoULD Study, Bae, Donald S, Goldfarb, Charles A, and Cook, Danielle L
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Prevention ,Perinatal Period - Conditions Originating in Perinatal Period ,Clinical Research ,Pediatric ,Diabetes ,Good Health and Well Being ,CoULD Study Group ,Congenital upper limb difference ,Gestational diabetes mellitus ,Gestational hypertension ,Maternal drug use ,Risk factors - Abstract
PurposeRisk factors for congenital upper limb differences (CoULDs) are often studied at the general population level. The CoULD registry provides a unique opportunity to study prenatal risk factors within a large patient sample.MethodsAll patients enrolled between June 2014 and March 2020 in the prospective CoULD registry, a national multicenter database of patients diagnosed with a CoULD, were included in the analysis. We analyzed self-reported, prenatal risk factors, including maternal smoking, alcohol use, recreational drug use, prescription drug use, gestational diabetes mellitus (GDM), and gestational hypertension. The outcome measures included comorbid medical conditions, proximal involvement of limb difference, bilateral involvement, and additional orthopedic conditions. Multivariable logistic regression was used to analyze the effect of the risk factors, controlling for sex and the presence of a named syndrome.ResultsIn total, 2,410 patients were analyzed, of whom 72% (1,734) did not have a self-reported risk factor. Among the 29% (676) who did have at least 1 risk factor, prenatal maternal prescription drug use was the most frequent (376/2,410; 16%). Maternal prescription drug use was associated with increased odds of patient medical comorbidities (odds ratio [OR] = 1.43, P = .02). Gestational diabetes mellitus was associated with increased odds of comorbid medical conditions (OR = 1.58, P = .04), additional orthopedic conditions (OR = 1.51, P = .04), and proximal involvement (OR = 1.52, P = .04). Overall, reporting 1 or more risk factors increased the odds of patient comorbid medical conditions (OR = 1.42, P < .001) and additional orthopedic conditions (OR = 1.25, P = .03).ConclusionsMost caregivers (72%) did not report a risk factor during enrollment. However, reporting a risk factor was associated with patient medical and orthopedic comorbidities. Of note, GDM alone significantly increased the odds of both these outcome measures along with proximal limb differences. These findings highlight the ill-defined etiology of CoULDs but suggest that prenatal risk factors, especially GDM, are associated with a higher degree of morbidity.Type of study/level of evidencePrognostic III.
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- 2022
17. Inhibiting a dynamic viral protease by targeting a non-catalytic cysteine
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Hulce, Kaitlin R, Jaishankar, Priyadarshini, Lee, Gregory M, Bohn, Markus-Frederik, Connelly, Emily J, Wucherer, Kristin, Ongpipattanakul, Chayanid, Volk, Regan F, Chuo, Shih-Wei, Arkin, Michelle R, Renslo, Adam R, and Craik, Charles S
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Biochemistry and Cell Biology ,Medicinal and Biomolecular Chemistry ,Chemical Sciences ,Biological Sciences ,Emerging Infectious Diseases ,Infectious Diseases ,5.1 Pharmaceuticals ,2.2 Factors relating to the physical environment ,Infection ,Cysteine ,Cytomegalovirus ,Cytomegalovirus Infections ,Humans ,Peptide Hydrolases ,Viral Proteases ,allostery ,antiviral ,conformational dynamics ,covalent inhibitor ,cytomegalovirus ,dimerization ,herpesvirus ,irreversible electrophile ,non-catalytic cysteine ,protease - Abstract
Viruses are responsible for some of the most deadly human diseases, yet available vaccines and antivirals address only a fraction of the potential viral human pathogens. Here, we provide a methodology for managing human herpesvirus (HHV) infection by covalently inactivating the HHV maturational protease via a conserved, non-catalytic cysteine (C161). Using human cytomegalovirus protease (HCMV Pr) as a model, we screened a library of disulfides to identify molecules that tether to C161 and inhibit proteolysis, then elaborated hits into irreversible HCMV Pr inhibitors that exhibit broad-spectrum inhibition of other HHV Pr homologs. We further developed an optimized tool compound targeted toward HCMV Pr and used an integrative structural biology and biochemical approach to demonstrate inhibitor stabilization of HCMV Pr homodimerization, exploiting a conformational equilibrium to block proteolysis. Irreversible HCMV Pr inhibition disrupts HCMV infectivity in cells, providing proof of principle for targeting proteolysis via a non-catalytic cysteine to manage viral infection.
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- 2022
18. Energy Services Interface: Requirements Document
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Brown, Richard, Khandekar, Aditya, Liu, Jingjing, Nordman, Bruce, Kolln, J, Widergren, S, Narang, D, Bohn, T, and Xue, Y
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- 2022
19. Pediatric Organ Dysfunction Information Update Mandate (PODIUM) Contemporary Organ Dysfunction Criteria: Executive Summary.
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Bembea, Melania, Agus, Michael, Akcan-Arikan, Ayse, Alexander, Peta, Basu, Rajit, Bennett, Tellen, Bohn, Desmond, Brandão, Leonardo, Brown, Ann-Marie, Carcillo, Joseph, Checchia, Paul, Cholette, Jill, Cheifetz, Ira, Cornell, Timothy, Doctor, Allan, Eckerle, Michelle, Erickson, Simon, Farris, Reid, Faustino, E, Fitzgerald, Julie, Fuhrman, Dana, Giuliano, John, Guilliams, Kristin, Gaies, Michael, Gorga, Stephen, Hall, Mark, Hanson, Sheila, Hartman, Mary, Hassinger, Amanda, Irving, Sharon, Jeffries, Howard, Jouvet, Philippe, Kannan, Sujatha, Karam, Oliver, Khemani, Robinder, Kissoon, Niranjan, Lacroix, Jacques, Laussen, Peter, Leclerc, Francis, Lee, Jan, Leteurtre, Stephane, Lobner, Katie, McKiernan, Patrick, Menon, Kusum, Monagle, Paul, Muszynski, Jennifer, Odetola, Folafoluwa, Parker, Robert, Pathan, Nazima, Pierce, Richard, Pineda, Jose, Prince, Jose, Robinson, Karen, Rowan, Courtney, Ryerson, Lindsay, Sanchez-Pinto, L, Schlapbach, Luregn, Selewski, David, Shekerdemian, Lara, Simon, Dennis, Smith, Lincoln, Squires, James, Squires, Robert, Sutherland, Scott, Ouellette, Yves, Spaeder, Michael, Srinivasan, Vijay, Steiner, Marie, Tasker, Robert, Thiagarajan, Ravi, Thomas, Neal, Tissieres, Pierre, Traube, Chani, Tucci, Marisa, Typpo, Katri, Wainwright, Mark, Ward, Shan, Watson, R, Weiss, Scott, Whitney, Jane, Willson, Doug, Wynn, James, Yehya, Nadir, and Zimmerman, Jerry
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Child ,Critical Care ,Critical Illness ,Evidence-Based Medicine ,Humans ,Multiple Organ Failure ,Organ Dysfunction Scores - Abstract
Prior criteria for organ dysfunction in critically ill children were based mainly on expert opinion. We convened the Pediatric Organ Dysfunction Information Update Mandate (PODIUM) expert panel to summarize data characterizing single and multiple organ dysfunction and to derive contemporary criteria for pediatric organ dysfunction. The panel was composed of 88 members representing 47 institutions and 7 countries. We conducted systematic reviews of the literature to derive evidence-based criteria for single organ dysfunction for neurologic, cardiovascular, respiratory, gastrointestinal, acute liver, renal, hematologic, coagulation, endocrine, endothelial, and immune system dysfunction. We searched PubMed and Embase from January 1992 to January 2020. Study identification was accomplished using a combination of medical subject headings terms and keywords related to concepts of pediatric organ dysfunction. Electronic searches were performed by medical librarians. Studies were eligible for inclusion if the authors reported original data collected in critically ill children; evaluated performance characteristics of scoring tools or clinical assessments for organ dysfunction; and assessed a patient-centered, clinically meaningful outcome. Data were abstracted from each included study into an electronic data extraction form. Risk of bias was assessed using the Quality in Prognosis Studies tool. Consensus was achieved for a final set of 43 criteria for pediatric organ dysfunction through iterative voting and discussion. Although the PODIUM criteria for organ dysfunction were limited by available evidence and will require validation, they provide a contemporary foundation for researchers to identify and study single and multiple organ dysfunction in critically ill children.
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- 2022
20. Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS
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Marotz, Clarisse, Molinsky, Rebecca, Martino, Cameron, Bohn, Bruno, Roy, Sumith, Rosenbaum, Michael, Desvarieux, Moïse, Yuzefpolskaya, Melana, Paster, Bruce J, Jacobs, David R, Colombo, Paolo C, Papapanou, Panos N, Knight, Rob, and Demmer, Ryan T
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Microbiology ,Biological Sciences ,Ecology ,Clinical Research ,Diabetes ,Infectious Diseases ,Dental/Oral and Craniofacial Disease ,Metabolic and endocrine ,Oral and gastrointestinal ,Good Health and Well Being ,Bacteria ,Cardiovascular Diseases ,Humans ,Microbiota ,Periodontitis ,Saliva - Abstract
Periodontitis affects up to 50% of individuals worldwide, and 8.5% are diagnosed with diabetes. The high-comorbidity rate of these diseases may suggest, at least in part, a shared etiology and pathophysiology. Changes in oral microbial communities have been documented in the context of severe periodontitis and diabetes, both independently and together. However, much less is known about the early oral microbial markers of these diseases. We used a subset of the ORIGINS project dataset, which collected detailed periodontal and cardiometabolic information from 787 healthy individuals, to identify early microbial markers of periodontitis and its association with markers of cardiometabolic health. Using state-of-the-art compositional data analysis tools, we identified the log-ratio of Treponema to Corynebacterium bacteria to be a novel Microbial Indicator of Periodontitis (MIP), and found that this MIP correlates with poor periodontal health and cardiometabolic markers early in disease pathogenesis in both subgingival plaque and saliva.
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- 2022
21. Feasibility of late acquisition [68Ga]Ga-PSMA-11 PET/CT using a long axial field-of-view PET/CT scanner for the diagnosis of recurrent prostate cancer-first clinical experiences.
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Alberts, Ian, Prenosil, George, Mingels, Clemens, Bohn, Karl, Viscione, Marco, Sari, Hasan, Rominger, Axel, and Afshar-Oromieh, Ali
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Digital PET ,PET/CT ,Positron-emission tomography ,Total body ,Ultra-long FOV PET ,Whole body ,Edetic Acid ,Feasibility Studies ,Humans ,Male ,Neoplasm Recurrence ,Local ,Positron Emission Tomography Computed Tomography ,Prostatic Neoplasms ,Retrospective Studies - Abstract
PURPOSE: While acquisition of images in [68 Ga]Ga-PSMA-11 following longer uptake times can improve lesion uptake and contrast, resultant imaging quality and count statistics are limited by the isotopes half-life (68 min). Here, we present a series of cases demonstrating that when performed using a long axial field-of-view (LAFOV) PET/CT system, late imaging is feasible and can even provide improved image quality compared to regular acquisitions. METHODS: In this retrospective case series, we report our initial experiences with 10 patients who underwent standard imaging at 1 h p.i. following administration of 192 ± 36 MBq [68 Ga]Ga-PSMA-11 with additional late imaging performed at 4 h p.i. Images were acquired in a single bed position for 6 min at 1 h p.i. and 16 min p.i. at 4 h p.i. using a LAFOV scanner (106 cm axial FOV). Two experienced nuclear medicine physicians reviewed all scans in consensus and evaluated overall image quality (5-point Likert scale), lesion uptake in terms of standardised uptake values (SUV), tumour to background ratio (TBR) and target-lesion signal to background noise (SNR). RESULTS: Subjective image quality as rated on a 5-point Likert scale was only modestly lower for late acquisitions (4.2/5 at 4 h p.i.; 5/5 1 h p.i.), TBR was significantly improved (4 h: 3.41 vs 1 h: 1.93, p
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- 2021
22. Immunotargeting of Nanocrystals by SpyCatcher Conjugation of Engineered Antibodies
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Pedroso, Cassio CS, Mann, Victor R, Zuberbühler, Kathrin, Bohn, Markus-Frederik, Yu, Jessica, Altoe, Virginia, Craik, Charles S, and Cohen, Bruce E
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Biological Sciences ,Biomedical and Clinical Sciences ,Industrial Biotechnology ,Women's Health ,Bioengineering ,Breast Cancer ,Cancer ,Biotechnology ,Nanotechnology ,1.1 Normal biological development and functioning ,Humans ,Receptors ,Urokinase Plasminogen Activator ,Antibodies ,Nanoparticles ,Cell Membrane ,Quantum Dots ,Urokinase-Type Plasminogen Activator ,bioconjugation ,upconverting nanoparticles ,quantum dots ,antibodies ,uPAR ,cancer cells ,receptor trafficking ,Nanoscience & Nanotechnology - Abstract
Inorganic nanocrystals such as quantum dots (QDs) and upconverting nanoparticles (UCNPs) are uniquely suited for quantitative live-cell imaging and are typically functionalized with ligands to study specific receptors or cellular targets. Antibodies (Ab) are among the most useful targeting reagents owing to their high affinities and specificities, but common nanocrystal labeling methods may orient Ab incorrectly, be reversible or denaturing, or lead to Ab-NP complexes too large for some applications. Here, we show that SpyCatcher proteins, which bind and spontaneously form covalent isopeptide bonds with cognate SpyTag peptides, can conjugate engineered Ab to nanoparticle surfaces with control over stability, orientation, and stoichiometry. Compact SpyCatcher-functionalized QDs and UCNPs may be labeled with short-chain variable fragment Ab (scFv) engineered to bind urokinase-type plasminogen activator receptors (uPAR) that are overexpressed in many human cancers. Confocal imaging of anti-uPAR scFv-QD conjugates shows the antibody mediates specific binding and internalization by breast cancer cells expressing uPAR. Time-lapse imaging of photostable scFv-UCNP conjugates shows that Ab binding causes uPAR internalization with a ∼20 min half-life on the cell surface, and uPAR is internalized to endolysosomal compartments distinct from general membrane stains and without significant recycling to the cell surface. The controlled and stable conjugation of engineered Ab to NPs enables targeting of diverse receptors for live-cell study of their distribution, trafficking, and physiology.
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- 2021
23. The influence of digital PET/CT on diagnostic certainty and interrater reliability in [68Ga]Ga-PSMA-11 PET/CT for recurrent prostate cancer.
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Alberts, Ian, Hünermund, Jan-Niklas, Sachpekidis, Christos, Mingels, Clemens, Fech, Viktor, Bohn, Karl, Rominger, Axel, and Afshar-Oromieh, Ali
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Molecular imaging ,Nuclear medicine ,Positron emission tomography ,Prostate cancer ,Edetic Acid ,Gallium Radioisotopes ,Humans ,Male ,Neoplasm Recurrence ,Local ,Positron Emission Tomography Computed Tomography ,Prostatic Neoplasms ,Reproducibility of Results ,Retrospective Studies - Abstract
OBJECTIVE: To investigate the impact of digital PET/CT on diagnostic certainty, patient-based sensitivity and interrater reliability. METHODS: Four physicians retrospectively evaluated two matched cohorts of patients undergoing [68Ga]Ga-PSMA-11 PET/CT on a digital (dPET/CT n = 65) or an analogue scanner (aPET/CT n = 65) for recurrent prostate cancer between 11/2018 and 03/2019. The number of equivocal and pathological lesions as well as the frequency of discrepant findings and the interrater reliability for the two scanners were compared. RESULTS: dPET/CT detected more lesions than aPET/CT (p < 0.001). A higher number of pathological scans were observed for dPET/CT (83% vs. 57%, p < 0.001). The true-positive rate at follow-up was 100% for dPET/CT compared to 84% for aPET/CT (p < 0.001). The proportion of lesions rated as non-pathological as a total of all PSMA-avid lesions detected for dPET/CT was comparable to aPET/CT (61.8% vs. 57.0%, p = 0.99). Neither a higher rate of diagnostically uncertain lesions (11.5% dPET/CT vs. 13.7% aPET/CT, p = 0.95) nor discrepant scans (where one or more readers differed in opinion as to whether the scan is pathological) were observed (18% dPET/CT vs. 17% aPET/CT, p = 0.76). Interrater reliability for pathological lesions was excellent for both scanner types (Cronbachs α = 0.923 dPET/CT; α = 0.948 aPET/CT) and interrater agreement was substantial for dPET/CT (Krippendorfs α = 0.701) and almost perfect in aPET/CT (α = 0.802). CONCLUSIONS: A higher detection rate for pathological lesions for dPET/CT compared with aPET/CT in multiple readers was observed. This improved sensitivity was coupled with an improved true-positive rate and was not associated with increased diagnostic uncertainty, rate of non-specific lesions, or reduced interrater reliability. KEY POINTS: • New generation digital scanners detect more cancer lesions in men with prostate cancer. • When using digital scanners, the doctors are able to diagnose prostate cancer lesions with better certainty • When using digital scanners, the doctors do not disagree with each other more than with other scanner types.
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- 2021
24. Comparing the diagnostic performance of radiotracers in recurrent prostate cancer: a systematic review and network meta-analysis.
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Alberts, Ian, Seide, Svenja, Mingels, Clemens, Bohn, Karl, Shi, Kuangyu, Zacho, Helle, Rominger, Axel, and Afshar-Oromieh, Ali
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Choline ,Comparative imaging ,Network meta-analysis ,PET/CT ,PSMA ,Positron emission tomography ,Radiotracers ,Bayes Theorem ,Copper Radioisotopes ,Glutarates ,Humans ,Male ,Neoplasm Recurrence ,Local ,Network Meta-Analysis ,Phosphinic Acids ,Positron Emission Tomography Computed Tomography ,Prostatic Neoplasms ,Pyridines - Abstract
PURPOSE: Many radiotracers are currently available for the detection of recurrent prostate cancer (rPC), yet many have not been compared head-to-head in comparative imaging studies. There is therefore an unmet need for evidence synthesis to guide evidence-based decisions in the selection of radiotracers. The objective of this study was therefore to assess the detection rate of various radiotracers for the rPC. METHODS: The PUBMED, EMBASE, and the EU and NIH trials databases were searched without date or language restriction for comparative imaging tracers for 13 radiotracers of principal interest. Key search terms included 18F-PSMA-1007, 18F-DCPFyl, 68Ga-PSMA-11, 18F-PSMA-11, 68Ga-PSMA-I&T, 68Ga-THP-PSMA, 64Cu-PSMA-617, 18F-JK-PSMA-7, 18F-Fluciclovine, 18F-FABC, 18F-Choline, 11C-Choline, and 68Ga-RM2. Studies reporting comparative imaging data in humans in rPC were selected. Single armed studies and matched pair analyses were excluded. Twelve studies with eight radiotracers were eligible for inclusion. Two independent reviewers screened all studies (using the PRISMA-NMA statement) for inclusion criteria, extracted data, and assessed risk of bias (using the QUADAS-2 tool). A network meta-analysis was performed using Markov-Chain Monte Carlo Bayesian analysis to obtain estimated detection rate odds ratios for each tracer combination. RESULTS: A majority of studies were judged to be at risk of publication bias. With the exception of 18F-PSMA-1007, little difference in terms of detection rate was revealed between the three most commonly used PSMA-radiotracers (68Ga-PSMA-11, 18F-PSMA-1007, 18F-DCFPyl), which in turn showed clear superiority to choline and fluciclovine using the derived network. CONCLUSION: Differences in patient-level detection rates were observed between PSMA- and choline-radiotracers. However, there is currently insufficient evidence to favour one of the four routinely used PSMA-radioligands (PSMA-11, PSMA-1007, PSMA-I&T, and DCFPyl) over another owing to the limited evidence base and risk of publication bias revealed by our systematic review. A further limitation was lack of reporting on diagnostic accuracy, which might favour radiotracers with low specificity in an analysis restricted only to detection rate. The NMA derived can be used to inform the design of future clinical trials and highlight areas where current evidence is weak.
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- 2021
25. The design, construction, and commissioning of the KATRIN experiment
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Aker, M, Altenmüller, K, Amsbaugh, JF, Arenz, M, Babutzka, M, Bast, J, Bauer, S, Bechtler, H, Beck, M, Beglarian, A, Behrens, J, Bender, B, Berendes, R, Berlev, A, Besserer, U, Bettin, C, Bieringer, B, Blaum, K, Block, F, Bobien, S, Böttcher, M, Bohn, J, Bokeloh, K, Bolz, H, Bornschein, B, Bornschein, L, Bouquet, H, Boyd, NM, Brunst, T, Burritt, TH, Caldwell, TS, Chaoui, Z, Chilingaryan, S, Choi, W, Corona, TJ, Cox, GA, Debowski, K, Deffert, M, Descher, M, Barrero, D Díaz, Doe, PJ, Dragoun, O, Drexlin, G, Dunmore, JA, Dyba, S, Edzards, F, Eichelhardt, F, Eitel, K, Ellinger, E, Engel, R, Enomoto, S, Erhard, M, Eversheim, D, Fedkevych, M, Felden, A, Fischer, S, Formaggio, JA, Fränkle, FM, Franklin, GB, Frenzel, H, Friedel, F, Fulst, A, Gauda, K, Gehring, R, Gil, W, Glück, F, Görhardt, S, Grimm, J, Grössle, R, Groh, S, Grohmann, S, Gumbsheimer, R, Hackenjos, M, Häßler, D, Hannen, V, Harms, F, Harper, GC, Hartmann, J, Haußmann, N, Heizmann, F, Helbing, K, Held, M, Hickford, S, Hilk, D, Hillen, B, Hiller, R, Hillesheimer, D, Hinz, D, Höhn, T, Hötzel, M, Holzmann, S, Horn, S, Houdy, T, Howe, MA, Huber, A, James, T, Jansen, A, Kaiser, M, Karl, C, and Kazachenko, O
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Nuclear and Plasma Physics ,Particle and High Energy Physics ,Physical Sciences ,Beam-line instrumentation ,Spectrometers ,Gas systems and purification ,Neutrino detectors ,Engineering ,Nuclear & Particles Physics ,Physical sciences - Abstract
The KArlsruhe TRItium Neutrino (KATRIN) experiment, which aims to make a direct and model-independent determination of the absolute neutrino mass scale, is a complex experiment with many components. More than 15 years ago, we published a technical design report (TDR) [1] to describe the hardware design and requirements to achieve our sensitivity goal of 0.2 eV at 90% C.L. on the neutrino mass. Since then there has been considerable progress, culminating in the publication of first neutrino mass results with the entire beamline operating [2]. In this paper, we document the current state of all completed beamline components (as of the first neutrino mass measurement campaign), demonstrate our ability to reliably and stably control them over long times, and present details on their respective commissioning campaigns.
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- 2021
26. A comprehensive review of imaging findings in COVID-19 - status in early 2021.
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Afshar-Oromieh, Ali, Prosch, Helmut, Schaefer-Prokop, Cornelia, Bohn, Karl, Alberts, Ian, Mingels, Clemens, Thurnher, Majda, Cumming, Paul, Shi, Kuangyu, Peters, Alan, Geleff, Silvana, Lan, Xiaoli, Wang, Feng, Huber, Adrian, Gräni, Christoph, Heverhagen, Johannes, Rominger, Axel, Fontanellaz, Matthias, Schöder, Heiko, Christe, Andreas, Mougiakakou, Stavroula, and Ebner, Lukas
- Subjects
COVID-19 ,Corona virus ,Imaging ,SARS-CoV-2 ,Artificial Intelligence ,COVID-19 ,Humans ,Pneumonia ,Viral ,Positron Emission Tomography Computed Tomography ,SARS-CoV-2 - Abstract
Medical imaging methods are assuming a greater role in the workup of patients with COVID-19, mainly in relation to the primary manifestation of pulmonary disease and the tissue distribution of the angiotensin-converting-enzyme 2 (ACE 2) receptor. However, the field is so new that no consensus view has emerged guiding clinical decisions to employ imaging procedures such as radiography, computer tomography (CT), positron emission tomography (PET), and magnetic resonance imaging, and in what measure the risk of exposure of staff to possible infection could be justified by the knowledge gained. The insensitivity of current RT-PCR methods for positive diagnosis is part of the rationale for resorting to imaging procedures. While CT is more sensitive than genetic testing in hospitalized patients, positive findings of ground glass opacities depend on the disease stage. There is sparse reporting on PET/CT with [18F]-FDG in COVID-19, but available results are congruent with the earlier literature on viral pneumonias. There is a high incidence of cerebral findings in COVID-19, and likewise evidence of gastrointestinal involvement. Artificial intelligence, notably machine learning is emerging as an effective method for diagnostic image analysis, with performance in the discriminative diagnosis of diagnosis of COVID-19 pneumonia comparable to that of human practitioners.
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- 2021
27. Clinical performance of long axial field of view PET/CT: a head-to-head intra-individual comparison of the Biograph Vision Quadra with the Biograph Vision PET/CT.
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Alberts, Ian, Hünermund, Jan-Niklas, Prenosil, George, Mingels, Clemens, Bohn, Karl, Viscione, Marco, Sari, Hasan, Vollnberg, Bernd, Shi, Kuangyu, Afshar-Oromieh, Ali, and Rominger, Axel
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Digital PET ,PET/CT ,Positron-emission-tomography ,Total-body ,Ultra-long FOV PET ,Whole-body ,Fluorodeoxyglucose F18 ,Humans ,Medical Oncology ,Motion ,Positron Emission Tomography Computed Tomography ,Positron-Emission Tomography ,Radiopharmaceuticals - Abstract
PURPOSE: To investigate the performance of the new long axial field-of-view (LAFOV) Biograph Vision Quadra PET/CT and a standard axial field-of-view (SAFOV) Biograph Vision 600 PET/CT (both: Siemens Healthineers) system using an intra-patient comparison. METHODS: Forty-four patients undergoing routine oncological PET/CT were prospectively included and underwent a same-day dual-scanning protocol following a single administration of either 18F-FDG (n = 20), 18F-PSMA-1007 (n = 16) or 68Ga-DOTA-TOC (n = 8). Half the patients first received a clinically routine examination on the SAFOV (FOVaxial 26.3 cm) in continuous bed motion and then immediately afterwards on the LAFOV system (10-min acquisition in list mode, FOVaxial 106 cm); the second half underwent scanning in the reverse order. Comparisons between the LAFOV at different emulated scan times (by rebinning list mode data) and the SAFOV were made for target lesion integral activity, signal to noise (SNR), target lesion to background ratio (TBR) and visual image quality. RESULTS: Equivalent target lesion integral activity to the SAFOV acquisitions (16-min duration for a 106 cm FOV) were obtained on the LAFOV in 1.63 ± 0.19 min (mean ± standard error). Equivalent SNR was obtained by 1.82 ± 1.00 min LAFOV acquisitions. No statistically significant differences (p > 0.05) in TBR were observed even for 0.5 min LAFOV examinations. Subjective image quality rated by two physicians confirmed the 10 min LAFOV to be of the highest quality, with equivalence between the LAFOV and the SAFOV at 1.8 ± 0.85 min. By analogy, if the LAFOV scans were maintained at 10 min, proportional reductions in applied radiopharmaceutical could obtain equivalent lesion integral activity for activities under 40 MBq and equivalent doses for the PET component of
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- 2021
28. Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia
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Asarnow, Daniel, Wang, Bei, Lee, Wen-Hsin, Hu, Yuanyu, Huang, Ching-Wen, Faust, Bryan, Ng, Patricia Miang Lon, Ngoh, Eve Zi Xian, Bohn, Markus, Bulkley, David, Pizzorno, Andrés, Ary, Beatrice, Tan, Hwee Ching, Lee, Chia Yin, Minhat, Rabiatul Adawiyah, Terrier, Olivier, Soh, Mun Kuen, Teo, Frannie Jiuyi, Yeap, Yvonne Yee Chin, Seah, Shirley Gek Kheng, Chan, Conrad En Zuo, Connelly, Emily, Young, Nicholas J, Maurer-Stroh, Sebastian, Renia, Laurent, Hanson, Brendon John, Rosa-Calatrava, Manuel, Manglik, Aashish, Cheng, Yifan, Craik, Charles S, and Wang, Cheng-I
- Subjects
Biomedical and Clinical Sciences ,Immunology ,Biodefense ,Coronaviruses ,Emerging Infectious Diseases ,Coronaviruses Therapeutics and Interventions ,Immunization ,Infectious Diseases ,Lung ,2.1 Biological and endogenous factors ,Infection ,Good Health and Well Being ,Angiotensin-Converting Enzyme 2 ,Animals ,Antibodies ,Neutralizing ,Antigen-Antibody Complex ,Binding Sites ,CHO Cells ,COVID-19 ,Cricetinae ,Cricetulus ,Cryoelectron Microscopy ,Giant Cells ,Humans ,Membrane Fusion ,Peptide Library ,Protein Binding ,Protein Domains ,Protein Structure ,Quaternary ,SARS-CoV-2 ,Spike Glycoprotein ,Coronavirus ,SARS-CoV ,Spike protein ,coronavirus ,phage display ,receptor binding domain ,recombinant monoclonal antibody ,syncytia ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by binding of the viral Spike protein to host receptor angiotensin-converting enzyme 2 (ACE2), followed by fusion of viral and host membranes. Although antibodies that block this interaction are in emergency use as early coronavirus disease 2019 (COVID-19) therapies, the precise determinants of neutralization potency remain unknown. We discovered a series of antibodies that potently block ACE2 binding but exhibit divergent neutralization efficacy against the live virus. Strikingly, these neutralizing antibodies can inhibit or enhance Spike-mediated membrane fusion and formation of syncytia, which are associated with chronic tissue damage in individuals with COVID-19. As revealed by cryoelectron microscopy, multiple structures of Spike-antibody complexes have distinct binding modes that not only block ACE2 binding but also alter the Spike protein conformational cycle triggered by ACE2 binding. We show that stabilization of different Spike conformations leads to modulation of Spike-mediated membrane fusion with profound implications for COVID-19 pathology and immunity.
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- 2021
29. Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia.
- Author
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Asarnow, Daniel, Wang, Bei, Lee, Wen-Hsin, Hu, Yuanyu, Huang, Ching-Wen, Faust, Bryan, Ng, Patricia Miang Lon, Ngoh, Eve Zi Xian, Bohn, Markus, Bulkley, David, Pizzorno, Andrés, Ary, Beatrice, Tan, Hwee Ching, Lee, Chia Yin, Minhat, Rabiatul Adawiyah, Terrier, Olivier, Soh, Mun Kuen, Teo, Frannie Jiuyi, Yeap, Yvonne Yee Chin, Seah, Shirley Gek Kheng, Chan, Conrad En Zuo, Connelly, Emily, Young, Nicholas J, Maurer-Stroh, Sebastian, Renia, Laurent, Hanson, Brendon John, Rosa-Calatrava, Manuel, Manglik, Aashish, Cheng, Yifan, Craik, Charles S, and Wang, Cheng-I
- Subjects
CHO Cells ,Giant Cells ,Animals ,Humans ,Cricetulus ,Peptide Library ,Antigen-Antibody Complex ,Cryoelectron Microscopy ,Membrane Fusion ,Binding Sites ,Protein Structure ,Quaternary ,Protein Binding ,Cricetinae ,Antibodies ,Neutralizing ,Spike Glycoprotein ,Coronavirus ,Protein Domains ,COVID-19 ,Angiotensin-Converting Enzyme 2 ,SARS-CoV-2 ,SARS-CoV ,Spike protein ,coronavirus ,phage display ,receptor binding domain ,recombinant monoclonal antibody ,syncytia ,Prevention ,Pneumonia & Influenza ,Biodefense ,Emerging Infectious Diseases ,Pneumonia ,Lung ,Infectious Diseases ,Vaccine Related ,2.1 Biological and endogenous factors ,Infection ,Developmental Biology ,Biological Sciences ,Medical and Health Sciences - Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by binding of the viral Spike protein to host receptor angiotensin-converting enzyme 2 (ACE2), followed by fusion of viral and host membranes. Although antibodies that block this interaction are in emergency use as early coronavirus disease 2019 (COVID-19) therapies, the precise determinants of neutralization potency remain unknown. We discovered a series of antibodies that potently block ACE2 binding but exhibit divergent neutralization efficacy against the live virus. Strikingly, these neutralizing antibodies can inhibit or enhance Spike-mediated membrane fusion and formation of syncytia, which are associated with chronic tissue damage in individuals with COVID-19. As revealed by cryoelectron microscopy, multiple structures of Spike-antibody complexes have distinct binding modes that not only block ACE2 binding but also alter the Spike protein conformational cycle triggered by ACE2 binding. We show that stabilization of different Spike conformations leads to modulation of Spike-mediated membrane fusion with profound implications for COVID-19 pathology and immunity.
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- 2021
30. Digital PET/CT allows for shorter acquisition protocols or reduced radiopharmaceutical dose in [18F]-FDG PET/CT.
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Alberts, Ian, Sachpekidis, Christos, Prenosil, George, Viscione, Marco, Bohn, Karl, Mingels, Clemens, Shi, Kuangyu, Ashar-Oromieh, Ali, and Rominger, Axel
- Subjects
Digital PET ,List mode acquisition ,PET/CT ,Positron emission tomography ,Body Weight ,Fluorodeoxyglucose F18 ,Humans ,Image Processing ,Computer-Assisted ,Neoplasms ,Positron Emission Tomography Computed Tomography ,Radiopharmaceuticals ,Retrospective Studies ,Sensitivity and Specificity ,Signal-To-Noise Ratio - Abstract
PURPOSE: To establish the feasibility of shorter acquisition times (and by analogy, applied activity) on tumour detection and lesion contrast in digital PET/CT. METHODS: Twenty-one randomly selected patients who underwent oncological [18F]-FDG PET/CT on a digital PET/CT were retrospectively evaluated. Scan data were anonymously obtained and reconstructed in list-mode acquisition for a standard 2 min/bed position (bp), 1 min/bp and 30 s/bp (100%, 50% and 25% time or applied activity, respectively). Scans were randomized and read by two nuclear medicine physicians in a consensus read. Readers were blind to clinical details. Scans were evaluated for the number of pathological lesions detected. Measured uptake for lesions was evaluated by maximum and mean standardized uptake value (SUVmax and SUVmean, respectively) and tumour-to-backround ratio (TBR) were compared. Agreement between the three acquisitions was compared by Krippendorfs alpha. RESULTS: Overall n = 100 lesions were identified in the 2 min and 1 min/bp acquisitions and n = 98 lesions in the 30 s/bp acquisitions. Agreement between the three acquisitions with respect to lesion number and tumour-to-background ratio showed almost perfect agreement (Ks α = 0.999). SUVmax, SUVmean and TBR likewise showed > 98% agreement, with longer acquisitions being associated with slightly higher mean TBR (2 min/bp 7.94 ± 4.41 versus 30 s/bp 7.84 ± 4.22, p
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- 2021
31. Structure of an affinity-matured inhibitory recombinant fab against urokinase plasminogen activator reveals basis of potency and specificity
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Sevillano, N, Bohn, MF, Zimanyi, M, Chen, Y, Petzold, C, Gupta, S, Ralston, CY, and Craik, CS
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Biochemistry and Cell Biology ,Biological Sciences ,5.1 Pharmaceuticals ,Amino Acid Sequence ,Humans ,Quinuclidines ,Recombinant Proteins ,Serine Endopeptidases ,Serine Proteases ,Serine Proteinase Inhibitors ,Urokinase-Type Plasminogen Activator ,uPA ,Recombinant antibody ,Protease inhibitor ,Affinity maturation ,Biochemistry & Molecular Biology ,Biophysics ,Biological sciences - Abstract
Affinity maturation of U33, a recombinant Fab inhibitor of uPA, was used to improve the affinity and the inhibitory effect compared to the parental Fab. Arginine scanning of the six CDR loops of U33 was done to identify initial binding determinants since uPA prefers arginine in its primary substrate binding pocket. Two CDR loops were selected to create an engineered affinity maturation library of U33 that was diversified around ArgL91 (CDR L3) and ArgH52 (CDR H2). Biopanning of the randomized U33 library under stringent conditions resulted in eight Fabs with improved binding properties. One of the most potent inhibitors, AB2, exhibited a 13-fold decrease in IC50 when compared to U33 largely due to a decrease in its off rate. To identify contributions of interfacial residues that might undergo structural rearrangement upon interface formation we used X-ray footprinting and mass spectrometry (XFMS). Four residues showed a pronounced decrease in solvent accessibility, and their clustering suggests that AB2 targets the active site and also engages residues in an adjacent pocket unique to human uPA. The 2.9 Å resolution crystal structure of AB2-bound to uPA shows a binding mode in which the CDR L1 loop inserts into the active site cleft and acts as a determinant of inhibition. The selectivity determinant of this binding mode is unlike previously identified inhibitory Fabs against uPA related serine proteases, MTSP-1, HGFA and FXIa. CDRs H2 and L3 loops aid in interface formation and provide critical salt-bridges to remodel loops surrounding the active site of uPA providing specificity and further evidence that antibodies can be potent and selective inhibitors of proteolytic enzymes.
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- 2021
32. Structure of an affinity-matured inhibitory recombinant fab against urokinase plasminogen activator reveals basis of potency and specificity.
- Author
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Sevillano, N, Bohn, MF, Zimanyi, M, Chen, Y, Petzold, C, Gupta, S, Ralston, CY, and Craik, CS
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Humans ,Quinuclidines ,Serine Endopeptidases ,Recombinant Proteins ,Serine Proteinase Inhibitors ,Amino Acid Sequence ,Urokinase-Type Plasminogen Activator ,Serine Proteases ,Affinity maturation ,Protease inhibitor ,Recombinant antibody ,uPA ,5.1 Pharmaceuticals ,Biophysics ,Biological Sciences ,Biochemistry & Molecular Biology - Abstract
Affinity maturation of U33, a recombinant Fab inhibitor of uPA, was used to improve the affinity and the inhibitory effect compared to the parental Fab. Arginine scanning of the six CDR loops of U33 was done to identify initial binding determinants since uPA prefers arginine in its primary substrate binding pocket. Two CDR loops were selected to create an engineered affinity maturation library of U33 that was diversified around ArgL91 (CDR L3) and ArgH52 (CDR H2). Biopanning of the randomized U33 library under stringent conditions resulted in eight Fabs with improved binding properties. One of the most potent inhibitors, AB2, exhibited a 13-fold decrease in IC50 when compared to U33 largely due to a decrease in its off rate. To identify contributions of interfacial residues that might undergo structural rearrangement upon interface formation we used X-ray footprinting and mass spectrometry (XFMS). Four residues showed a pronounced decrease in solvent accessibility, and their clustering suggests that AB2 targets the active site and also engages residues in an adjacent pocket unique to human uPA. The 2.9 Å resolution crystal structure of AB2-bound to uPA shows a binding mode in which the CDR L1 loop inserts into the active site cleft and acts as a determinant of inhibition. The selectivity determinant of this binding mode is unlike previously identified inhibitory Fabs against uPA related serine proteases, MTSP-1, HGFA and FXIa. CDRs H2 and L3 loops aid in interface formation and provide critical salt-bridges to remodel loops surrounding the active site of uPA providing specificity and further evidence that antibodies can be potent and selective inhibitors of proteolytic enzymes.
- Published
- 2021
33. Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage
- Author
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Rillo-Bohn, Regina, Adilardi, Renzo, Mitros, Therese, Avşaroğlu, Barış, Stevens, Lewis, Koehler, Simone, Bayes, Joshua, Wang, Clara, Lin, Sabrina, Baskevitch, Kayla Alienor, Rokhsar, Daniel S, and Dernburg, Abby F
- Subjects
Biological Sciences ,Genetics ,Biotechnology ,Underpinning research ,1.1 Normal biological development and functioning ,Generic health relevance ,Animals ,Chromosome Pairing ,Chromosome Segregation ,Crossing Over ,Genetic ,Endodeoxyribonucleases ,Gene Expression Regulation ,Developmental ,Male ,Models ,Genetic ,Rad51 Recombinase ,Rhabditida ,pristionchus pacificus ,meiosis ,meiotic recombination ,chromosome pairing ,comparative cell biology ,Other ,cell biology ,genetics ,genomics ,Biochemistry and Cell Biology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Meiosis is conserved across eukaryotes yet varies in the details of its execution. Here we describe a new comparative model system for molecular analysis of meiosis, the nematode Pristionchus pacificus, a distant relative of the widely studied model organism Caenorhabditis elegans. P. pacificus shares many anatomical and other features that facilitate analysis of meiosis in C. elegans. However, while C. elegans has lost the meiosis-specific recombinase Dmc1 and evolved a recombination-independent mechanism to synapse its chromosomes, P. pacificus expresses both DMC-1 and RAD-51. We find that SPO-11 and DMC-1 are required for stable homolog pairing, synapsis, and crossover formation, while RAD-51 is dispensable for these key meiotic processes. RAD-51 and DMC-1 localize sequentially to chromosomes during meiotic prophase and show nonoverlapping functions. We also present a new genetic map for P. pacificus that reveals a crossover landscape very similar to that of C. elegans, despite marked divergence in the regulation of synapsis and crossing-over between these lineages.
- Published
- 2021
34. A compendium of community engagement responses to the COVID-19 pandemic
- Author
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Eder, Milton Mickey, Ralston, Penny, Millender, Eugenia, Speights, Joedrecka S Brown, De Leon, Jessica, Wiehe, Sarah, Claxton, Gina, Savaiano, Dennis, Himmelfarb, Cheryl Dennison, Ahmed, Syed, Nelson, David, Brown, Jen, Kandula, Namratha, Tandon, Darius, Thomas, Ariel, AuYoung, Mona, Chen, Wei-ting, Stewart, M Kate, Zender, Robynn, Brown, Arleen F, Carson, Savanna L, Morris, D’Ann, Vassar, Stefanie D, Von Jaeger, Rodney, Taras, Howard, Nguyen, Francisco Tung, Palmer, Nynikka, Fleisher, Paula, Cabrera, Abby, Wong, Erica, Harrison, James, Potter, Mike, Grumbach, Kevin, Cottler, Linda, Millay, Tamara, Striley, Catherine, Mudd, Gia, Eder, Milton, Monsen, Karen, Austin, Robin, Jones, Clarence, Sugarwala, Laura, Cullen, John, Orlando, Elissa, Bennett, Nancy, Kubicek, Katrina, Kipke, Michelle, Croisant, Sharon A, Singleton, Chantele, Prochaska, John, Bohn, Krista, Millay, Tamara A, and Cottler, Linda B
- Subjects
Health Services and Systems ,Health Sciences ,Infectious Diseases ,Coronaviruses ,Cancer ,Clinical Research ,Generic health relevance ,Community engagement ,community-engaged research ,Translational Science ,disparities ,trust ,COVID-19 ,CTSA ,PACER - Abstract
IntroductionClinical and Translational Science Award Program (CTSA)-funded institutions were charged with developing clinical and translational science programs and transforming clinical research at their institutions. Community engagement (CE) was recognized as a key component and catalyst of that transformation. CE hub capacities for working with communities and translating knowledge into practice have been illustrated through their COVID-19 responses.MethodsCE hub leaders met and discussed their CTSA's early responses regarding the COVID-19 pandemic. The 2-hour discussion was distilled into themes which were sent to the CE hub leaders with a request for written accounts describing actions taken to engage local partners, communities, and institutions. The written reports form the basis for this compendium.ResultsEighteen institutions submitted written reports describing activities in relation to six themes: (1) listen to the community and respond to concerns, (2) collect data to understand the impact of COVID-19 on distinct communities and groups, (3) communicate science and address misinformation, (4) collaborate with health departments, (5) engage hubs and underrepresented populations in COVID-19 research, and (6) support our own well-being and that of others.ConclusionsBidirectional interactions comprise the foundation of CE, which requires trusted partnerships that sustain communication through a series of activities and goals. The nimble responses to the pandemic substantiate the need for CE programs to maintain the infrastructure necessary to achieve the primary CTSA goals of improving health within and across communities and localities as well as expanding research participation of community members.
- Published
- 2021
35. A Longitudinal Study of Great Ape Cognition: Stability, Reliability and the Influence of Individual Characteristics
- Author
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Bohn, Manuel, Eckert, Johanna, Hanus, Daniel, and Haun, Daniel Benjamin Moritz
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cognitive science - Abstract
Primate cognition research allows us to reconstruct the evolution of human cognition. However, temporal and contextual factors that induce variation in cognitive studies with great apes are poorly understood. Here we report on a longitudinal study where we repeatedly tested a comparatively large sample of great apes (N = 40) with the same set of cognitive measures. We investigated the stability of group-level results, the reliability of individual differences, and the relation between cognitive performance and individual-level characteristics. We found results to be relatively stable on a group level. Some, but not all, tasks showed acceptable levels of reliability. Cognitive performance across tasks was not systematically related to any particular individual-level predictor. This study highlights the importance of methodological considerations – especially when studying individual differences – on the route to building a more robust science of primate cognitive evolution.
- Published
- 2021
36. Genetic interaction mapping informs integrative structure determination of protein complexes
- Author
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Braberg, Hannes, Echeverria, Ignacia, Bohn, Stefan, Cimermancic, Peter, Shiver, Anthony, Alexander, Richard, Xu, Jiewei, Shales, Michael, Dronamraju, Raghuvar, Jiang, Shuangying, Dwivedi, Gajendradhar, Bogdanoff, Derek, Chaung, Kaitlin K, Hüttenhain, Ruth, Wang, Shuyi, Mavor, David, Pellarin, Riccardo, Schneidman, Dina, Bader, Joel S, Fraser, James S, Morris, John, Haber, James E, Strahl, Brian D, Gross, Carol A, Dai, Junbiao, Boeke, Jef D, Sali, Andrej, and Krogan, Nevan J
- Subjects
Biochemistry and Cell Biology ,Bioinformatics and Computational Biology ,Biological Sciences ,Genetics ,Bioengineering ,1.1 Normal biological development and functioning ,2.1 Biological and endogenous factors ,Generic health relevance ,Histones ,Multiprotein Complexes ,Mutation ,Protein Conformation ,Protein Interaction Mapping ,Protein Interaction Maps ,Saccharomyces cerevisiae ,Saccharomyces cerevisiae Proteins ,General Science & Technology - Abstract
Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on ~500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations.
- Published
- 2020
37. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
- Author
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Gordon, David E, Jang, Gwendolyn M, Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, White, Kris M, O’Meara, Matthew J, Rezelj, Veronica V, Guo, Jeffrey Z, Swaney, Danielle L, Tummino, Tia A, Hüttenhain, Ruth, Kaake, Robyn M, Richards, Alicia L, Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J, Braberg, Hannes, Fabius, Jacqueline M, Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J, Cakir, Merve, McGregor, Michael J, Li, Qiongyu, Meyer, Bjoern, Roesch, Ferdinand, Vallet, Thomas, Mac Kain, Alice, Miorin, Lisa, Moreno, Elena, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Shi, Ying, Zhang, Ziyang, Shen, Wenqi, Kirby, Ilsa T, Melnyk, James E, Chorba, John S, Lou, Kevin, Dai, Shizhong A, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Lyu, Jiankun, Mathy, Christopher JP, Perica, Tina, Pilla, Kala Bharath, Ganesan, Sai J, Saltzberg, Daniel J, Rakesh, Ramachandran, Liu, Xi, Rosenthal, Sara B, Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Huang, Xi-Ping, Liu, YongFeng, Wankowicz, Stephanie A, Bohn, Markus, Safari, Maliheh, Ugur, Fatima S, Koh, Cassandra, Savar, Nastaran Sadat, Tran, Quang Dinh, Shengjuler, Djoshkun, Fletcher, Sabrina J, O’Neal, Michael C, Cai, Yiming, Chang, Jason CJ, Broadhurst, David J, Klippsten, Saker, Sharp, Phillip P, Wenzell, Nicole A, Kuzuoglu-Ozturk, Duygu, Wang, Hao-Yuan, Trenker, Raphael, Young, Janet M, Cavero, Devin A, Hiatt, Joseph, Roth, Theodore L, Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Stroud, Robert M, Frankel, Alan D, Rosenberg, Oren S, Verba, Kliment A, Agard, David A, Ott, Melanie, Emerman, Michael, and Jura, Natalia
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Emerging Infectious Diseases ,Coronaviruses ,Infectious Diseases ,Coronaviruses Therapeutics and Interventions ,5.1 Pharmaceuticals ,Infection ,Good Health and Well Being ,Animals ,Antiviral Agents ,Betacoronavirus ,COVID-19 ,Chlorocebus aethiops ,Cloning ,Molecular ,Coronavirus Infections ,Drug Evaluation ,Preclinical ,Drug Repositioning ,HEK293 Cells ,Host-Pathogen Interactions ,Humans ,Immunity ,Innate ,Mass Spectrometry ,Molecular Targeted Therapy ,Pandemics ,Pneumonia ,Viral ,Protein Binding ,Protein Biosynthesis ,Protein Domains ,Protein Interaction Mapping ,Protein Interaction Maps ,Receptors ,sigma ,SARS-CoV-2 ,SKP Cullin F-Box Protein Ligases ,Vero Cells ,Viral Proteins ,COVID-19 Drug Treatment ,General Science & Technology - Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
- Published
- 2020
38. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
- Author
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Gordon, David E, Jang, Gwendolyn M, Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, White, Kris M, O’Meara, Matthew J, Rezelj, Veronica V, Guo, Jeffrey Z, Swaney, Danielle L, Tummino, Tia A, Hüttenhain, Ruth, Kaake, Robyn M, Richards, Alicia L, Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J, Braberg, Hannes, Fabius, Jacqueline M, Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J, Cakir, Merve, McGregor, Michael J, Li, Qiongyu, Meyer, Bjoern, Roesch, Ferdinand, Vallet, Thomas, Mac Kain, Alice, Miorin, Lisa, Moreno, Elena, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Shi, Ying, Zhang, Ziyang, Shen, Wenqi, Kirby, Ilsa T, Melnyk, James E, Chorba, John S, Lou, Kevin, Dai, Shizhong A, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Lyu, Jiankun, Mathy, Christopher JP, Perica, Tina, Pilla, Kala Bharath, Ganesan, Sai J, Saltzberg, Daniel J, Rakesh, Ramachandran, Liu, Xi, Rosenthal, Sara B, Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Huang, Xi-Ping, Liu, YongFeng, Wankowicz, Stephanie A, Bohn, Markus, Safari, Maliheh, Ugur, Fatima S, Koh, Cassandra, Savar, Nastaran Sadat, Tran, Quang Dinh, Shengjuler, Djoshkun, Fletcher, Sabrina J, O’Neal, Michael C, Cai, Yiming, Chang, Jason CJ, Broadhurst, David J, Klippsten, Saker, Sharp, Phillip P, Wenzell, Nicole A, Kuzuoglu-Ozturk, Duygu, Wang, Hao-Yuan, Trenker, Raphael, Young, Janet M, Cavero, Devin A, Hiatt, Joseph, Roth, Theodore L, Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Stroud, Robert M, Frankel, Alan D, Rosenberg, Oren S, Verba, Kliment A, Agard, David A, Ott, Melanie, Emerman, Michael, and Jura, Natalia
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Pneumonia ,Emerging Infectious Diseases ,Rare Diseases ,Biodefense ,Orphan Drug ,Vaccine Related ,Infectious Diseases ,Immunization ,Prevention ,Pneumonia & Influenza ,Lung ,5.1 Pharmaceuticals ,Development of treatments and therapeutic interventions ,Infection ,Good Health and Well Being ,Animals ,Antiviral Agents ,Betacoronavirus ,COVID-19 ,Chlorocebus aethiops ,Cloning ,Molecular ,Coronavirus Infections ,Drug Evaluation ,Preclinical ,Drug Repositioning ,HEK293 Cells ,Host-Pathogen Interactions ,Humans ,Immunity ,Innate ,Mass Spectrometry ,Molecular Targeted Therapy ,Pandemics ,Pneumonia ,Viral ,Protein Binding ,Protein Biosynthesis ,Protein Domains ,Protein Interaction Mapping ,Protein Interaction Maps ,Receptors ,sigma ,SARS-CoV-2 ,SKP Cullin F-Box Protein Ligases ,Vero Cells ,Viral Proteins ,COVID-19 Drug Treatment ,General Science & Technology - Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
- Published
- 2020
39. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
- Author
-
Gordon, David E, Jang, Gwendolyn M, Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, White, Kris M, O'Meara, Matthew J, Rezelj, Veronica V, Guo, Jeffrey Z, Swaney, Danielle L, Tummino, Tia A, Hüttenhain, Ruth, Kaake, Robyn M, Richards, Alicia L, Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J, Braberg, Hannes, Fabius, Jacqueline M, Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J, Cakir, Merve, McGregor, Michael J, Li, Qiongyu, Meyer, Bjoern, Roesch, Ferdinand, Vallet, Thomas, Mac Kain, Alice, Miorin, Lisa, Moreno, Elena, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Shi, Ying, Zhang, Ziyang, Shen, Wenqi, Kirby, Ilsa T, Melnyk, James E, Chorba, John S, Lou, Kevin, Dai, Shizhong A, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Lyu, Jiankun, Mathy, Christopher JP, Perica, Tina, Pilla, Kala Bharath, Ganesan, Sai J, Saltzberg, Daniel J, Rakesh, Ramachandran, Liu, Xi, Rosenthal, Sara B, Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Huang, Xi-Ping, Liu, YongFeng, Wankowicz, Stephanie A, Bohn, Markus, Safari, Maliheh, Ugur, Fatima S, Koh, Cassandra, Savar, Nastaran Sadat, Tran, Quang Dinh, Shengjuler, Djoshkun, Fletcher, Sabrina J, O'Neal, Michael C, Cai, Yiming, Chang, Jason CJ, Broadhurst, David J, Klippsten, Saker, Sharp, Phillip P, Wenzell, Nicole A, Kuzuoglu-Ozturk, Duygu, Wang, Hao-Yuan, Trenker, Raphael, Young, Janet M, Cavero, Devin A, Hiatt, Joseph, Roth, Theodore L, Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Stroud, Robert M, Frankel, Alan D, Rosenberg, Oren S, Verba, Kliment A, Agard, David A, Ott, Melanie, Emerman, Michael, and Jura, Natalia
- Subjects
Vero Cells ,Animals ,Humans ,Pneumonia ,Viral ,Coronavirus Infections ,SKP Cullin F-Box Protein Ligases ,Receptors ,sigma ,Viral Proteins ,Antiviral Agents ,Drug Evaluation ,Preclinical ,Cloning ,Molecular ,Protein Interaction Mapping ,Protein Biosynthesis ,Protein Binding ,Mass Spectrometry ,Host-Pathogen Interactions ,Immunity ,Innate ,HEK293 Cells ,Drug Repositioning ,Pandemics ,Molecular Targeted Therapy ,Protein Interaction Maps ,Protein Domains ,Betacoronavirus ,Chlorocebus aethiops ,COVID-19 ,SARS-CoV-2 ,General Science & Technology - Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
- Published
- 2020
40. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
- Author
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Gordon, David E, Jang, Gwendolyn M, Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, O'Meara, Matthew J, Guo, Jeffrey Z, Swaney, Danielle L, Tummino, Tia A, Hüttenhain, Ruth, Kaake, Robyn M, Richards, Alicia L, Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J, Braberg, Hannes, Fabius, Jacqueline M, Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J, Cakir, Merve, McGregor, Michael J, Li, Qiongyu, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Kirby, Ilsa T, Melnyk, James E, Chorba, John S, Lou, Kevin, Dai, Shizhong A, Shen, Wenqi, Shi, Ying, Zhang, Ziyang, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Mathy, Christopher JP, Perica, Tina, Pilla, Kala B, Ganesan, Sai J, Saltzberg, Daniel J, Ramachandran, Rakesh, Liu, Xi, Rosenthal, Sara B, Calviello, Lorenzo, Venkataramanan, Srivats, Lin, Yizhu, Wankowicz, Stephanie A, Bohn, Markus, Trenker, Raphael, Young, Janet M, Cavero, Devin, Hiatt, Joe, Roth, Theo, Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Roesch, Ferdinand, Vallet, Thomas, Meyer, Björn, White, Kris M, Miorin, Lisa, Agard, David, Emerman, Michael, Ruggero, Davide, García-Sastre, Adolfo, Jura, Natalia, von Zastrow, Mark, Taunton, Jack, Schwartz, Olivier, Vignuzzi, Marco, d'Enfert, Christophe, Mukherjee, Shaeri, Jacobson, Matt, Malik, Harmit S, Fujimori, Danica G, Ideker, Trey, Craik, Charles S, Floor, Stephen, Fraser, James S, Gross, John, Sali, Andrej, Kortemme, Tanja, Beltrao, Pedro, Shokat, Kevan, Shoichet, Brian K, and Krogan, Nevan J
- Subjects
Prevention ,Vaccine Related ,Biodefense ,Infectious Diseases ,Rare Diseases ,Pneumonia & Influenza ,Emerging Infectious Diseases ,Lung ,Pneumonia ,5.1 Pharmaceuticals ,2.2 Factors relating to the physical environment ,Infection - Abstract
An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity- purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
- Published
- 2020
41. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
- Author
-
Gordon, David E, Jang, Gwendolyn M, Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, O'Meara, Matthew J, Guo, Jeffrey Z, Swaney, Danielle L, Tummino, Tia A, Huettenhain, Ruth, Kaake, Robyn M, Richards, Alicia L, Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J, Braberg, Hannes, Fabius, Jacqueline M, Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J, Cakir, Merve, McGregor, Michael J, Li, Qiongyu, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Kirby, Ilsa T, Melnyk, James E, Chorba, John S, Lou, Kevin, Dai, Shizhong A, Shen, Wenqi, Shi, Ying, Zhang, Ziyang, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Mathy, Christopher JP, Perica, Tina, Pilla, Kala B, Ganesan, Sai J, Saltzberg, Daniel J, Ramachandran, Rakesh, Liu, Xi, Rosenthal, Sara B, Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Wankowicz, Stephanie A, Bohn, Markus, Sharp, Phillip P, Trenker, Raphael, Young, Janet M, Cavero, Devin A, Hiatt, Joseph, Roth, Theodore L, Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Roesch, Ferdinand, Vallet, Thomas, Meyer, Björn, White, Kris M, Miorin, Lisa, Rosenberg, Oren S, Verba, Kliment A, Agard, David, Ott, Melanie, Emerman, Michael, Ruggero, Davide, García-Sastre, Adolfo, Jura, Natalia, von Zastrow, Mark, Taunton, Jack, Ashworth, Alan, Schwartz, Olivier, Vignuzzi, Marco, d'Enfert, Christophe, Mukherjee, Shaeri, Jacobson, Matt, Malik, Harmit S, Fujimori, Danica G, Ideker, Trey, Craik, Charles S, Floor, Stephen, Fraser, James S, Gross, John, Sali, Andrej, Kortemme, Tanja, Beltrao, Pedro, Shokat, Kevan, Shoichet, Brian K, and Krogan, Nevan J
- Subjects
Medical Microbiology ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Biological Sciences ,Coronaviruses ,Emerging Infectious Diseases ,Infectious Diseases ,2.2 Factors relating to the physical environment ,5.1 Pharmaceuticals ,Infection ,Good Health and Well Being - Abstract
An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity- purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
- Published
- 2020
42. When do workarounds help or hurt patient outcomes? The moderating role of operational failures
- Author
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Tucker, Anita L, Zheng, Sarah, Gardner, John W, and Bohn, Roger E
- Subjects
Clinical Research ,Health Services ,Patient Safety ,Health and social care services research ,8.1 Organisation and delivery of services ,Generic health relevance ,healthcare cost ,medical error ,operational failures ,survey ,workarounds ,Mathematical Sciences ,Engineering ,Commerce ,Management ,Tourism and Services ,Business & Management - Published
- 2020
43. When do workarounds help or hurt patient outcomes? The moderating role of operational failures
- Author
-
Tucker, Anita L, Zheng, Sarah, Gardner, John W, and Bohn, Roger E
- Subjects
healthcare cost ,medical error ,operational failures ,survey ,workarounds ,Health Services ,Patient Safety ,Clinical Research ,8.1 Organisation and delivery of services ,Generic Health Relevance ,Mathematical Sciences ,Engineering ,Commerce ,Management ,Tourism and Services ,Business & Management ,Commerce ,Management ,Tourism and Services - Published
- 2020
44. Specificity for latent C termini links the E3 ubiquitin ligase CHIP to caspases
- Author
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Ravalin, Matthew, Theofilas, Panagiotis, Basu, Koli, Opoku-Nsiah, Kwadwo A, Assimon, Victoria A, Medina-Cleghorn, Daniel, Chen, Yi-Fan, Bohn, Markus F, Arkin, Michelle, Grinberg, Lea T, Craik, Charles S, and Gestwicki, Jason E
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Brain Disorders ,Aging ,Neurodegenerative ,Dementia ,Acquired Cognitive Impairment ,Neurosciences ,Alzheimer's Disease ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Neurological ,Caspases ,Cell Line ,Tumor ,Crystallography ,X-Ray ,Escherichia coli ,Gene Expression Regulation ,Humans ,Protein Binding ,Ubiquitin ,Ubiquitin-Activating Enzymes ,Ubiquitin-Protein Ligases ,Ubiquitination ,Medicinal and Biomolecular Chemistry ,Biochemistry & Molecular Biology ,Biochemistry and cell biology ,Medicinal and biomolecular chemistry - Abstract
Protein-protein interactions between E3 ubiquitin ligases and protein termini help shape the proteome. These interactions are sensitive to proteolysis, which alters the ensemble of cellular N and C termini. Here we describe a mechanism wherein caspase activity reveals latent C termini that are then recognized by the E3 ubiquitin ligase CHIP. Using expanded knowledge of CHIP's binding specificity, we predicted hundreds of putative interactions arising from caspase activity. Subsequent validation experiments confirmed that CHIP binds the latent C termini at tauD421 and caspase-6D179. CHIP binding to tauD421, but not tauFL, promoted its ubiquitination, while binding to caspase-6D179 mediated ubiquitin-independent inhibition. Given that caspase activity generates tauD421 in Alzheimer's disease (AD), these results suggested a concise model for CHIP regulation of tau homeostasis. Indeed, we find that loss of CHIP expression in AD coincides with the accumulation of tauD421 and caspase-6D179. These results illustrate an unanticipated link between caspases and protein homeostasis.
- Published
- 2019
45. Reduced blood oxygenation level dependent connectivity is related to hypoperfusion in Alzheimer’s disease
- Author
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Göttler, Jens, Preibisch, Christine, Riederer, Isabelle, Pasquini, Lorenzo, Alexopoulos, Panagiotis, Bohn, Karl Peter, Yakushev, Igor, Beller, Ebba, Kaczmarz, Stephan, Zimmer, Claus, Grimmer, Timo, Drzezga, Alexander, and Sorg, Christian
- Subjects
Biomedical and Clinical Sciences ,Neurosciences ,Clinical Sciences ,Biomedical Imaging ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Acquired Cognitive Impairment ,Clinical Research ,Aging ,Neurodegenerative ,Bioengineering ,Brain Disorders ,Dementia ,Alzheimer's Disease ,Neurological ,Aged ,Aged ,80 and over ,Alzheimer Disease ,Brain ,Cerebrovascular Circulation ,Female ,Fluorodeoxyglucose F18 ,Hemodynamics ,Humans ,Magnetic Resonance Imaging ,Male ,Middle Aged ,Neurons ,Oxygen ,Positron-Emission Tomography ,Signal Transduction ,Alzheimer's disease ,resting-state fMRI ,blood oxygenation level dependent-functional connectivity ,arterial spin labeling ,F-18-fluorodeoxyglucose-positron emission tomography ,Alzheimer’s disease ,F-fluorodeoxyglucose-positron emission tomography ,Cardiorespiratory Medicine and Haematology ,Neurology & Neurosurgery ,Clinical sciences - Abstract
Functional connectivity of blood oxygenation level dependent signal fluctuations (BOLD-FC) is decreased in Alzheimer's disease (AD), and suggested to reflect reduced coherence in neural population activity; however, as both neuronal and vascular-hemodynamic processes underlie BOLD signals, impaired perfusion might also contribute to reduced BOLD-FC; 42 AD patients and 27 controls underwent simultaneous PET/MR imaging. Resting-state functional MRI assessed BOLD co-activity to quantify BOLD-FC, pulsed arterial spin labeling (pASL) assessed cerebral blood flow (CBF) as proxy for vascular hemodynamics, and 18F-fluorodeoxyglucose PET assessed glucose metabolism (GluMet) to index neuronal activity. Patients' BOLD-FC, CBF, and GluMet were reduced within the same precuneal parietal regions. BOLD-FC was positively associated with mean CBF, specifically in patients and controlled for GluMet levels, suggesting that BOLD-FC reductions correlate with pASL-derived hypoperfusion in AD, independently from 18F-fluorodeoxyglucose PET-derived hypometabolism. Data indicate that impaired vascular hemodynamic processes contribute to reduced BOLD connectivity in AD.
- Published
- 2019
46. IMMIGRATION AND DEMOGRAPHICS: CAN HIGH IMMIGRANT FERTILITY EXPLAIN VOTER SUPPORT FOR IMMIGRATION?
- Author
-
Bohn, Henning and Lopez-Velasco, Armando R
- Subjects
Behavioral and Social Science ,Basic Behavioral and Social Science ,Immigration ,Political Economy Model ,Overlapping Generations ,Immigrant Fertility Rates ,Intergenerational Redistribution ,Economic Theory ,Applied Economics ,Econometrics ,Economics - Abstract
First generation immigrants to the United States have higher fertility rates than natives. This paper analyzes to what extent this factor provides political support for immigration, using an overlapping generation model with production and capital accumulation. In this setting, immigration represents a dynamic trade-off for native workers as more immigrants decrease current wages but increase the future return on their savings. We find that immigrant fertility has surprisingly strong effects on voter incentives, especially when there is persistence in the political process. If fertility rates are sufficiently high, native workers support immigration. Persistence, either due to inertia induced by frictions in the legal system or through expectational linkages, significantly magnifies the effects. Entry of immigrants with high fertility has redistributive impacts across generations similar to pay-as-you-go social security: initial generations are net winners, whereas later generations are net losers.
- Published
- 2019
47. IMMIGRATION AND DEMOGRAPHICS: CAN HIGH IMMIGRANT FERTILITY EXPLAIN VOTER SUPPORT FOR IMMIGRATION?
- Author
-
Bohn, Henning and Lopez-Velasco, Armando R
- Subjects
Immigration ,Political Economy Model ,Overlapping Generations ,Immigrant Fertility Rates ,Intergenerational Redistribution ,Basic Behavioral and Social Science ,Behavioral and Social Science ,Economic Theory ,Economics - Abstract
First generation immigrants to the United States have higher fertility rates than natives. This paper analyzes to what extent this factor provides political support for immigration, using an overlapping generation model with production and capital accumulation. In this setting, immigration represents a dynamic trade-off for native workers as more immigrants decrease current wages but increase the future return on their savings. We find that immigrant fertility has surprisingly strong effects on voter incentives, especially when there is persistence in the political process. If fertility rates are sufficiently high, native workers support immigration. Persistence, either due to inertia induced by frictions in the legal system or through expectational linkages, significantly magnifies the effects. Entry of immigrants with high fertility has redistributive impacts across generations similar to pay-as-you-go social security: initial generations are net winners, whereas later generations are net losers.
- Published
- 2019
48. Integrating Common Ground and Informativeness in Pragmatic Word Learning
- Author
-
Bohn, Manuel, Tessler, Michael Henry, and Frank, Michael C.
- Subjects
Pragmatics ,Word learning ,Common ground ,Bayesian models - Abstract
Pragmatic inferences are an integral part of language learn-ing and comprehension. To recover the intended meaning ofan utterance, listeners need to balance and integrate differentsources of contextual information. In a series of experiments,we studied how listeners integrate general expectations aboutspeakers with expectations specific to their interactional his-tory with a particular speaker. We used a Bayesian pragmaticsmodel to formalize the integration process. In Experiments1 and 2, we replicated previous findings showing that listenersmake inferences based on speaker-general and speaker-specificexpectations. We then used the empirical measurements fromthese experiments to generate model predictions about howthe two kinds of expectations should be integrated, which wetested in Experiment 3. Experiment 4 replicated and extendedExperiment 3 to a broader set of conditions. In both experi-ments, listeners based their inferences on both types of expec-tations. We found that model performance was also consistentwith this finding; with better fit for a model which incorporatedboth general and specific information compared to baselinesincorporating only one type. Listeners flexibly integrate dif-ferent forms of social expectations across a range of contexts,a process which can be described using Bayesian models ofpragmatic reasoning.
- Published
- 2019
49. Intergenerational mobility and the political economy of immigration
- Author
-
Bohn, Henning and Lopez-Velasco, Armando R
- Subjects
Immigration ,Political economy model ,Overlapping generations ,Intergenerational mobility ,Guest workers ,Economic Theory ,Applied Economics ,Banking ,Finance and Investment ,Economics - Published
- 2018
50. Intergenerational mobility and the political economy of immigration
- Author
-
Bohn, Henning and Lopez-Velasco, Armando R
- Subjects
Immigration ,Political economy model ,Overlapping generations ,Intergenerational mobility ,Guest workers ,Economics ,Economic Theory ,Applied Economics ,Banking ,Finance and Investment - Published
- 2018
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