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  • Lu, San, et al. (author)
  • Magnetotail reconnection onset caused by electron kinetics with a strong external driver
  • 2020
  • In: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
  • Journal article (peer-reviewed)abstract
    • Magnetotail reconnection plays a crucial role in explosive energy conversion in geospace. Because of the lack of in-situ spacecraft observations, the onset mechanism of magnetotail reconnection, however, has been controversial for decades. The key question is whether magnetotail reconnection is externally driven to occur first on electron scales or spontaneously arising from an unstable configuration on ion scales. Here, we show, using spacecraft observations and particle-in-cell (PIC) simulations, that magnetotail reconnection starts from electron reconnection in the presence of a strong external driver. Our PIC simulations show that this electron reconnection then develops into ion reconnection. These results provide direct evidence for magnetotail reconnection onset caused by electron kinetics with a strong external driver.
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  • Wang, Rongsheng, et al. (author)
  • Asymmetry in the current sheet and secondary magnetic flux ropes during guide field magnetic reconnection
  • 2012
  • In: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 117, s. A07223-
  • Journal article (peer-reviewed)abstract
    • A magnetic reconnection event with a moderate guide field encountered by Cluster in the near-Earth tail on 28 August 2002 is reported. The guide field points dawnward during this event. The quadrupolar structure of the Hall magnetic field within the ion diffusion region is distorted toward the northern hemisphere in the earthward part while toward the southern hemisphere tailward part of X-line. Observations of current density and electron pitch angle distribution indicate that the distorted quadrupolar structure is formed due to a deformed Hall electron current system. Cluster crossed the ion diffusion region from south to north earthward of the X-line. An electron density cavity is confirmed in the northern separatrix layer while a thin current layer (TCL) is measured in the southern separatrix layer. The TCL is formed due to electrons injected into the X-line along the magnetic field. These observations are different from simulation results where the cavity is produced associated with inflow electrons along the southern separatrix while the strong current sheet appears with the outflow electron beam along the northern separatrix. The energy of the inflowing electron in the separatrix layer could extend up to 10 keV. Energetic electron fluxes up to 50 keV have a clear peak in the TCL. The length of the separatrix layer is estimated to be at least 65 c/omega(pi). These observations suggest that electrons could be pre-accelerated before they are ejected into the X-line region along the separatrix. Multiple secondary flux ropes moving earthward are observed within the diffusion region. These secondary flux ropes are all identified earthward of the observed TCL. These observations further suggest there are numerous small scale structures within the ion diffusion region.
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  • Brownstein, Catherine A., et al. (author)
  • An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
  • 2014
  • In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
  • Journal article (peer-reviewed)abstract
    • Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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  • Giralt, Sergio, et al. (author)
  • American Society of Blood and Marrow Transplantation, European Society of Blood and Marrow Transplantation, Blood and Marrow Transplant Clinical Trials Network, and International Myeloma Working Group Consensus Conference on Salvage Hematopoietic Cell Transplantation in Patients with Relapsed Multiple Myeloma.
  • 2015
  • In: Biology of Blood and Marrow Transplantation. - : Elsevier BV. - 1083-8791. ; 21:12, s. 2039-2051
  • Journal article (peer-reviewed)abstract
    • In contrast to the upfront setting in which the role of high-dose therapy with autologous hematopoietic cell transplantation (HCT) as consolidation of a first remission in patients with multiple myeloma (MM) is well established, the role of high-dose therapy with autologous or allogeneic HCT has not been extensively studied in MM patients relapsing after primary therapy. The International Myeloma Working Group together with the Blood and Marrow Transplant Clinical Trials Network, the American Society of Blood and Marrow Transplantation, and the European Society of Blood and Marrow Transplantation convened a meeting of MM experts to: (1) summarize current knowledge regarding the role of autologous or allogeneic HCT in MM patients progressing after primary therapy, (2) propose guidelines for the use of salvage HCT in MM, (3) identify knowledge gaps, (4) propose a research agenda, and (5) develop a collaborative initiative to move the research agenda forward. After reviewing the available data, the expert committee came to the following consensus statement for salvage autologous HCT: (1) In transplantation-eligible patients relapsing after primary therapy that did NOT include an autologous HCT, high-dose therapy with HCT as part of salvage therapy should be considered standard; (2) High-dose therapy and autologous HCT should be considered appropriate therapy for any patients relapsing after primary therapy that includes an autologous HCT with initial remission duration of more than 18 months; (3) High-dose therapy and autologous HCT can be used as a bridging strategy to allogeneic HCT; (4) The role of postsalvage HCT maintenance needs to be explored in the context of well-designed prospective trials that should include new agents, such as monoclonal antibodies, immune-modulating agents, and oral proteasome inhibitors; (5) Autologous HCT consolidation should be explored as a strategy to develop novel conditioning regimens or post-HCT strategies in patients with short (less than 18 months remissions) after primary therapy; and (6) Prospective randomized trials need to be performed to define the role of salvage autologous HCT in patients with MM relapsing after primary therapy comparing it to "best non-HCT" therapy. The expert committee also underscored the importance of collecting enough hematopoietic stem cells to perform 2 transplantations early in the course of the disease. Regarding allogeneic HCT, the expert committee agreed on the following consensus statements: (1) Allogeneic HCT should be considered appropriate therapy for any eligible patient with early relapse (less than 24 months) after primary therapy that included an autologous HCT and/or high-risk features (ie, cytogenetics, extramedullary disease, plasma cell leukemia, or high lactate dehydrogenase); (2) Allogeneic HCT should be performed in the context of a clinical trial if possible; (3) The role of postallogeneic HCT maintenance therapy needs to be explored in the context of well-designed prospective trials; and (4) Prospective randomized trials need to be performed to define the role salvage allogeneic HCT in patients with MM relapsing after primary therapy.
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  • Kohls, Mirjam, et al. (author)
  • Impact of cumulative body mass index and cardiometabolic diseases on survival among patients with colorectal and breast cancer : a multi-centre cohort study
  • 2022
  • In: BMC Cancer. - : BioMed Central (BMC). - 1471-2407. ; 22:1
  • Journal article (peer-reviewed)abstract
    • Background: Body mass index (BMI) and cardiometabolic comorbidities such as cardiovascular disease and type 2 diabetes have been studied as negative prognostic factors in cancer survival, but possible dependencies in the mechanisms underlying these associations remain largely unexplored. We analysed these associations in colorectal and breast cancer patients.Methods: Based on repeated BMI assessments of cancer-free participants from four European countries in the European Prospective Investigation into Cancer and nutrition (EPIC) study, individual BMI-trajectories reflecting predicted mean BMI between ages 20 to 50 years were estimated using a growth curve model. Participants with incident colorectal or breast cancer after the age of 50 years were included in the survival analysis to study the prognostic effect of mean BMI and cardiometabolic diseases (CMD) prior to cancer. CMD were defined as one or more chronic conditions among stroke, myocardial infarction, and type 2 diabetes. Hazard ratios (HRs) and confidence intervals (CIs) of mean BMI and CMD were derived using multivariable-adjusted Cox proportional hazard regression for mean BMI and CMD separately and both exposures combined, in subgroups of localised and advanced disease.Results: In the total cohort of 159,045 participants, there were 1,045 and 1,620 eligible patients of colorectal and breast cancer. In colorectal cancer patients, a higher BMI (by 1 kg/m2) was associated with a 6% increase in risk of death (95% CI of HR: 1.02–1.10). The HR for CMD was 1.25 (95% CI: 0.97–1.61). The associations for both exposures were stronger in patients with localised colorectal cancer. In breast cancer patients, a higher BMI was associated with a 4% increase in risk of death (95% CI: 1.00–1.08). CMDs were associated with a 46% increase in risk of death (95% CI: 1.01–2.09). The estimates and CIs for BMI remained similar after adjustment for CMD and vice versa.Conclusions: Our results suggest that cumulative exposure to higher BMI during early to mid-adulthood was associated with poorer survival in patients with breast and colorectal cancer, independent of CMD prior to cancer diagnosis. The association between a CMD diagnosis prior to cancer and survival in patients with breast and colorectal cancer was independent of BMI.
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  • Lu, Sai San Moon, et al. (author)
  • Antibiotics Use and Subsequent Risk of Colorectal Cancer : A Swedish Nationwide Population-Based Study
  • 2022
  • In: Journal of the National Cancer Institute. - : Oxford University Press. - 0027-8874 .- 1460-2105. ; 114:1, s. 38-46
  • Journal article (peer-reviewed)abstract
    • BACKGROUND: Antibiotics use may increase colorectal cancer (CRC) risk by altering the gut microbiota, with suggestive evidence reported. Our study aims to investigate antibiotics use in relation to subsequent CRC risk.METHODS: This is a nationwide, population-based study with a matched case-control design (first primary CRC cases and 5 matched, cancer-free controls). Complete-population data, extracted from Swedish national registers for the period 2005-2016, were used to calculate odds ratios and 95% confidence intervals.RESULTS: We included 40 545 CRC cases and 202 720 controls. Using the full dataset, we found a positive association between more frequent antibiotics use and CRC, excluding antibiotics prescribed within 2 years of diagnosis attenuated results toward the null. In site-specific analyses, excluding the 2-year washout, the positive association was confined to the proximal colon (adjusted odds ratio for very high use vs no use = 1.17, 95% confidence interval = 1.05 to 1.31). For rectal cancer, an inverse association, which appears to be driven by women, was observed. Quinolones and sulfonamides and/or trimethoprims were positively associated with proximal colon cancer, whereas a more general inverse association, across antibiotics classes, was observed for rectal cancer. We found no association between methenamine hippurate, a urinary tract antiseptic not affecting the gut microbiota, and CRC risk.CONCLUSIONS: This register-based study covering the entire population of Sweden found a robust association between antibiotics use and higher risk of proximal colon cancer and an inverse association with rectal cancer in women. This study strengthens the evidence from previous investigations and adds important insight into site-specific colorectal carcinogenesis.
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  • Lu, Sai San Moon, 1988- (author)
  • Antibiotics use in relation to colorectal cancer risk, survival and postoperative complications
  • 2024
  • Doctoral thesis (other academic/artistic)abstract
    • Background: Growing evidence suggests that antibiotic-induced dysbiosis of gut microbiota potentially contributes to colorectal cancer development and oncological outcomes. However, the role of antibiotics in colorectal cancer incidence, survival and postoperative outcomes at a population level remains incompletely understood.Aims: The overall aim of the thesis is to investigate prescription antibiotics use in relation to colorectal cancer risk, survival and postoperative complications, particularly surgical site infections including anastomotic leakage.Methods: The thesis work includes matched case-control and cohort studies, leveraging complete population-based data from Swedish national registers. Paper I is a matched case-control study that consists of 40 545 colorectal cancer cases and 202 720 matched controls, aiming to investigate antibiotics use and risk of incident colorectal cancer. Multivariable conditional logistic regression was used. Paper II is a cohort study, including 47 303 colorectal cancer cases, investigating antibiotics use in relation to cancer-specific survival. Stratified Cox proportional-hazards regression was used. Paper III includes 38 839 colorectal cancer cases who had undergone abdominal tumour-resection surgery and assesses antibiotics use in relation to surgical site infections, including anastomotic leakage, within 30 days after surgery. Logistic regression with multi-level mixed-effects models was used.Results: In paper I, a dose-response association between antibiotics use and a higher risk of proximal colon cancer was found, whereas a slight inverse association with rectal cancer was observed, mainly in women. A null association was found between methenamine hippurate, assessed as a negative control due to no known effect on gut microbiome, and the risk of colorectal cancer. In paper II, the findings did not support any substantial negative effect of antibiotics on cancer-specific survival, except for very high cumulative exposure (>180 days) in stage I-III diseases. In stage IV colorectal cancer, modest inverse relationships between antibiotics use and survival were noted. In paper III, prescription antibiotics use up to 4.5 years before surgery was associated with a higher risk of surgical site infections, including anastomotic leakage, after colon cancer surgery but not rectal cancer surgery. A null association was observed between methanamine hippurate and the risk of surgical site infections. For cardiovascular and/or neurological complications, also considered as a negative control due to expected negligible or null effects of gut microbiome on these outcomes after surgery, associations were null in both colon and rectal cancer.Conclusion: These studies provided further support for antibiotics use as a modifiable risk factor for proximal colon cancer and identified antibiotics taken long before surgery as a novel risk factor for surgical site infections, including anastomotic leakage, after colon cancer surgery. In contrast, we did not find any substantial negative impact of antibiotics on cancer-specific survival. Taken together, the findings described in this thesis provide etiological insights and may contribute to strategies to prevent colon cancer and improve postoperative outcomes through prudent use of antibiotics, thereby aiding in the reduction of colorectal cancer incidence and mortality.
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  • Lu, Sai San Moon, et al. (author)
  • Inequalities in early childhood mortality in Myanmar : Association between parents' socioeconomic status and early childhood mortality
  • 2019
  • In: Global Health Action. - : Taylor & Francis Group. - 1654-9716 .- 1654-9880. ; 12:1
  • Journal article (peer-reviewed)abstract
    • Background: Despite global achievements in reducing early childhood mortality, disparities remain. There have been empirical studies of inequalities conducted in low- and middle-income countries. However, there have been no epidemiological studies on socioeconomic inequalities and early childhood survival in Myanmar.Objective: To estimate associations between two measures of parental socioeconomic status - household wealth and education - and age-specific early childhood mortality in Myanmar.Methods: Using cross-sectional data obtained from the Myanmar Demographic Health Survey (2015-2016), univariate and multiple logistic regressions were performed to investigate associations between household wealth and highest attained parental education, and under-5, neonatal, post-neonatal and child mortality. Data for 10,081 children born to 5,932 married women (aged 15-49 years) 10 years prior to the survey, were analysed.Results: Mortality during the first five years was associated with household wealth. In multiple logistic models, wealth was protective for post-neonatal mortality. After adjusting for individual proximate determinants, the odds of post-neonatal mortality in the richest households were 85% lower (95% CI: 50-96%) than in the poorest households. However, significant association was not found between wealth and neonatal mortality. Parental education was important for early childhood mortality; the highest benefit from parental education was for child mortality in the one- to five-year age bracket. After adjusting for proximate determinants, children with a higher educated parent had 95% (95% CI 77-99%) lower odds of death in this age group compared with children whose parents' highest educational attainment was at primary level. The association between parental education and neonatal mortality was not significant.Conclusions: In Myanmar, household wealth and parental education are important for childhood survival before five years of age. This study identified nuanced age-related differences in associations. Health policy must take socioeconomic determinants into account in order to address unfair inequalities in early childhood mortality.
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  • Lu, Sai San Moon, et al. (author)
  • Prediagnostic prescription antibiotics use and survival in patients with colorectal cancer : a swedish national register-based study
  • 2023
  • In: Cancer Epidemiology, Biomarkers and Prevention. - : American Association For Cancer Research (AACR). - 1055-9965 .- 1538-7755. ; 32:10, s. 1391-1401
  • Journal article (peer-reviewed)abstract
    • BACKGROUND: Antibiotics use is associated with higher colorectal cancer risk, but little is known regarding any potential effects on survival.METHODS: We conducted a nationwide cohort study, using complete-population data from Swedish national registers between 2005 and 2020, to investigate prediagnostic prescription antibiotics use in relation to survival in colorectal cancer patients.RESULTS: We identified 36,061 stage I-III and 11,242 stage IV colorectal cancer cases diagnosed between 2010 and 2019. For stage I-III, any antibiotics use (binary yes/no variable) was not associated with overall or cancer-specific survival. Compared with no use, moderate antibiotics use (total 11-60 days) was associated with slightly better cancer-specific survival [adjusted HR (aHR) = 0.93; 95% confidence interval (CI), 0.86-0.99)], whereas very high use (>180 days) was associated with worse survival [overall survival (OS) aHR = 1.42; 95% CI, 1.26-1.60, cancer-specific survival aHR = 1.31; 95% CI, 1.10-1.55]. In analyses by different antibiotic types, although not statistically significant, worse survival outcomes were generally observed across several antibiotics, particularly macrolides and/or lincosamides. In stage IV colorectal cancer, inverse relationships between antibiotics use and survival were noted.CONCLUSIONS: Overall, our findings do not support any substantial detrimental effects of prediagnostic prescription antibiotics use on cancer-specific survival after colorectal cancer diagnosis, with the possible exception of very high use in stage I-III colorectal cancer. Further investigation is warranted to confirm and understand these results.IMPACT: Although the study findings require confirmation, physicians probably do not need to factor in prediagnostic prescription antibiotics use in prognosticating patients with colorectal cancer.
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  • Pham, Thu Thi, et al. (author)
  • Pre-diagnostic circulating resistin concentrations and mortality among individuals with colorectal cancer : results from the european prospective investigation into cancer and nutrition study
  • 2024
  • In: International Journal of Cancer. - : John Wiley & Sons. - 0020-7136 .- 1097-0215. ; 154:9, s. 1596-1606
  • Journal article (peer-reviewed)abstract
    • Resistin is a protein involved in inflammation and angiogenesis processes and may play a role in the progression of colorectal cancer (CRC). However, it remains unclear whether resistin is associated with increased mortality after CRC diagnosis. We examined pre-diagnostic serum resistin concentrations in relation to CRC-specific and all-cause mortality among 1343 incident CRC cases from the European Prospective Investigation into Cancer and Nutrition cohort. For CRC-specific mortality as the primary outcome, hazard ratios (HRs) and 95% confidence intervals (95% CI) were estimated from competing risk analyses based on cause-specific Cox proportional hazards models and further in sensitivity analyses using Fine–Gray proportional subdistribution hazards models. For all-cause mortality as the secondary outcome, Cox proportional hazards models were used. Subgroup analyses were performed by sex, tumor subsite, tumor stage, body mass index and time to CRC diagnosis. Resistin was measured on a median of 4.8 years before CRC diagnosis. During a median follow-up of 8.2 years, 474 deaths from CRC and 147 deaths from other causes were observed. Resistin concentrations were not associated with CRC-specific mortality (HRQ4vsQ1 = 0.95, 95% CI: 0.73–1.23; Ptrend =.97; and HRper doubling of resistin concentration = 1.00; 95% CI: 0.84–1.19; P =.98) or all-cause mortality. Results from competing risk (sensitivity) analysis were similar. No associations were found in any subgroup analyses. These findings suggest no association between pre-diagnostic circulating resistin concentrations and CRC-specific or all-cause mortality among persons with CRC, and the potential insignificance of resistin in CRC progression.
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  • Richards, Stephen, et al. (author)
  • Genome Sequence of the Pea Aphid Acyrthosiphon pisum
  • 2010
  • In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
  • Journal article (peer-reviewed)abstract
    • Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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  • Richards, Stephen, et al. (author)
  • The genome of the model beetle and pest Tribolium castaneum.
  • 2008
  • In: Nature. - 1476-4687. ; 452:7190, s. 949-55
  • Journal article (peer-reviewed)abstract
    • Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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  • Skinbjerg, Mette, et al. (author)
  • D2 dopamine receptor internalization prolongs the decrease of radioligand binding after amphetamine : a PET study in a receptor internalization-deficient mouse model
  • 2010
  • In: NeuroImage. - : Elsevier. - 1053-8119 .- 1095-9572. ; 50:4, s. 1402-1407
  • Journal article (peer-reviewed)abstract
    • Dopamine released by amphetamine decreases the in vivo binding of PET radioligands to the dopamine D(2) receptor. Although concentrations of extracellular dopamine largely return to baseline within 1 to 2 h after amphetamine treatment, radioligand binding remains decreased for several hours. The purpose of this study was to determine whether the prolonged decrease of radioligand binding after amphetamine administration is caused by receptor internalization. To distinguish dopamine displacement from receptor internalization, we used wild-type and arrestin3 (arr3) knockout mice, which are incapable of internalizing D(2) receptors. In addition, we used both the D(2) selective agonist [(11)C]MNPA (which is thought to bind to the high affinity state of the receptor) and the D(2) selective antagonist [(18)F]fallypride (which does not differentiate between high and low affinity state). After an initial baseline scan, animals were divided in three groups for a second scan: either 30 min or 4 h after amphetamine administration (3 mg/kg, i.p.) or as retest. At 30 min, [(11)C]MNPA showed greater displacement than [(18)F]fallypride, but each radioligand gave similar displacement in knockout and wild-type mice. At 4 h, the binding of both radioligands returned to baseline in arr3 knockout mice, but remained decreased in wild-type mice. Radioligand binding was unaltered on retest scanning. Our results suggest that the prolonged decrease of radioligand binding after amphetamine is mainly due to internalization of the D(2) receptor rather than dopamine displacement. In addition, this study demonstrates the utility of small animal PET to study receptor trafficking in vivo in genetically modified mice.
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