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A Deep Learning-Based Integrated Framework for Quality-Aware Undersampled Cine Cardiac MRI Reconstruction and Analysis. IEEE Trans Biomed Eng 2024; 71:855-865. [PMID: 37782583 DOI: 10.1109/tbme.2023.3321431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Cine cardiac magnetic resonance (CMR) imaging is considered the gold standard for cardiac function evaluation. However, cine CMR acquisition is inherently slow and in recent decades considerable effort has been put into accelerating scan times without compromising image quality or the accuracy of derived results. In this article, we present a fully-automated, quality-controlled integrated framework for reconstruction, segmentation and downstream analysis of undersampled cine CMR data. The framework produces high quality reconstructions and segmentations, leading to undersampling factors that are optimised on a scan-by-scan basis. This results in reduced scan times and automated analysis, enabling robust and accurate estimation of functional biomarkers. To demonstrate the feasibility of the proposed approach, we perform simulations of radial k-space acquisitions using in-vivo cine CMR data from 270 subjects from the UK Biobank (with synthetic phase) and in-vivo cine CMR data from 16 healthy subjects (with real phase). The results demonstrate that the optimal undersampling factor varies for different subjects by approximately 1 to 2 seconds per slice. We show that our method can produce quality-controlled images in a mean scan time reduced from 12 to 4 seconds per slice, and that image quality is sufficient to allow clinically relevant parameters to be automatically estimated to lie within 5% mean absolute difference.
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Targeting Solid Cancers with a Cancer-Specific Monoclonal Antibody to Surface Expressed Aberrantly O-glycosylated Proteins. Mol Cancer Ther 2023; 22:1204-1214. [PMID: 37451822 PMCID: PMC10543972 DOI: 10.1158/1535-7163.mct-23-0221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/14/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The lack of antibodies with sufficient cancer selectivity is currently limiting the treatment of solid tumors by immunotherapies. Most current immunotherapeutic targets are tumor-associated antigens that are also found in healthy tissues and often do not display sufficient cancer selectivity to be used as targets for potent antibody-based immunotherapeutic treatments, such as chimeric antigen receptor (CAR) T cells. Many solid tumors, however, display aberrant glycosylation that results in expression of tumor-associated carbohydrate antigens that are distinct from healthy tissues. Targeting aberrantly glycosylated glycopeptide epitopes within existing or novel glycoprotein targets may provide the cancer selectivity needed for immunotherapy of solid tumors. However, to date only a few such glycopeptide epitopes have been targeted. Here, we used O-glycoproteomics data from multiple cell lines to identify a glycopeptide epitope in CD44v6, a cancer-associated CD44 isoform, and developed a cancer-specific mAb, 4C8, through a glycopeptide immunization strategy. 4C8 selectively binds to Tn-glycosylated CD44v6 in a site-specific manner with low nanomolar affinity. 4C8 was shown to be highly cancer specific by IHC of sections from multiple healthy and cancerous tissues. 4C8 CAR T cells demonstrated target-specific cytotoxicity in vitro and significant tumor regression and increased survival in vivo. Importantly, 4C8 CAR T cells were able to selectively kill target cells in a mixed organotypic skin cancer model having abundant CD44v6 expression without affecting healthy keratinocytes, indicating tolerability and safety.
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Engaging an HIV vaccine target through the acquisition of low B cell affinity. Nat Commun 2023; 14:5249. [PMID: 37640732 PMCID: PMC10462694 DOI: 10.1038/s41467-023-40918-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Low affinity is common for germline B cell receptors (BCR) seeding development of broadly neutralizing antibodies (bnAbs) that engage hypervariable viruses, including HIV. Antibody affinity selection is also non-homogenizing, insuring the survival of low affinity B cell clones. To explore whether this provides a natural window for expanding human B cell lineages against conserved vaccine targets, we deploy transgenic mice mimicking human antibody diversity and somatic hypermutation (SHM) and immunize with simple monomeric HIV glycoprotein envelope immunogens. We report an immunization regimen that focuses B cell memory upon the conserved CD4 binding site (CD4bs) through both conventional affinity maturation and reproducible expansion of low affinity BCR clones with public patterns in SHM. In the latter instance, SHM facilitates target acquisition by decreasing binding strength. This suggests that permissive B cell selection enables the discovery of antibody epitopes, in this case an HIV bnAb site.
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Abstract
The cyclic oligonucleotide-based antiphage signalling system (CBASS) and the pyrimidine cyclase system for antiphage resistance (Pycsar) are antiphage defence systems in diverse bacteria that use cyclic nucleotide signals to induce cell death and prevent viral propagation1,2. Phages use several strategies to defeat host CRISPR and restriction-modification systems3-10, but no mechanisms are known to evade CBASS and Pycsar immunity. Here we show that phages encode anti-CBASS (Acb) and anti-Pycsar (Apyc) proteins that counteract defence by specifically degrading cyclic nucleotide signals that activate host immunity. Using a biochemical screen of 57 phages in Escherichia coli and Bacillus subtilis, we discover Acb1 from phage T4 and Apyc1 from phage SBSphiJ as founding members of distinct families of immune evasion proteins. Crystal structures of Acb1 in complex with 3'3'-cyclic GMP-AMP define a mechanism of metal-independent hydrolysis 3' of adenosine bases, enabling broad recognition and degradation of cyclic dinucleotide and trinucleotide CBASS signals. Structures of Apyc1 reveal a metal-dependent cyclic NMP phosphodiesterase that uses relaxed specificity to target Pycsar cyclic pyrimidine mononucleotide signals. We show that Acb1 and Apyc1 block downstream effector activation and protect from CBASS and Pycsar defence in vivo. Active Acb1 and Apyc1 enzymes are conserved in phylogenetically diverse phages, demonstrating that cleavage of host cyclic nucleotide signals is a key strategy of immune evasion in phage biology.
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Abstract
We present PRETUS - a Plugin-based Real Time UltraSound software platform for live ultrasound image analysis and operator support. The software is lightweight; functionality is brought in via independent plug-ins that can be arranged in sequence. The software allows to capture the real-time stream of ultrasound images from virtually any ultrasound machine, applies computational methods and visualizes the results on-the-fly. Plug-ins can run concurrently without blocking each other. They can be implemented in C++ and Python. A graphical user interface can be implemented for each plug-in, and presented to the user in a compact way. The software is free and open source, and allows for rapid prototyping and testing of real-time ultrasound imaging methods in a manufacturer-agnostic fashion. The software is provided with input, output and processing plug-ins, as well as with tutorials to illustrate how to develop new plug-ins for PRETUS.
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Mapping of truncated O-glycans in cancers of epithelial and non-epithelial origin. Br J Cancer 2021; 125:1239-1250. [PMID: 34526666 DOI: 10.1038/s41416-021-01530-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 07/08/2021] [Accepted: 08/17/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Novel immunotherapies targeting cancer-associated truncated O-glycans Tn (GalNAcα-Ser/Thr) and STn (Neu5Acα2-6GalNacα-Ser/Thr) are promising strategies for cancer treatment. However, no comprehensive, antibody-based mapping of truncated O-glycans in tumours exist to guide drug development. METHODS We used monoclonal antibodies to map the expression of truncated O-glycans in >700 tissue cores representing healthy and tumour tissues originating from breast, colon, lung, pancreas, skin, CNS and mesenchymal tissue. Patient-derived xenografts were used to evaluate Tn expression upon tumour engraftment. RESULTS The Tn-antigen was highly expressed in breast (57%, n = 64), colorectal (51%, n = 140) and pancreatic (53%, n = 108) tumours, while STn was mainly observed in colorectal (80%, n = 140) and pancreatic (56%, n = 108) tumours. We observed no truncated O-glycans in mesenchymal tumours (n = 32) and low expression of Tn (5%, n = 87) and STn (1%, n = 75) in CNS tumours. No Tn-antigen was found in normal tissue (n = 124) while STn was occasionally observed in healthy gastrointestinal tissue. Surface expression of Tn-antigen was identified across several cancers. Tn and STn expression decreased with tumour grade, but not with cancer stage. Numerous xenografts maintained Tn expression. CONCLUSIONS Surface expression of truncated O-glycans is limited to cancers of epithelial origin, making Tn and STn attractive immunological targets in the treatment of human carcinomas.
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Automatic orientation cues for intuitive immersive interrogation of 3D echocardiographic images in virtual reality using deep learning. Eur Heart J Cardiovasc Imaging 2021. [DOI: 10.1093/ehjci/jeaa356.407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: Other. Main funding source(s): NIHR i4i funded 3D Heart Project Wellcome / EPSRC Centre for Medical Engineering (WT 203148/Z/16/Z)
onbehalf
3D Heart Project
Background/Introduction:
In echocardiography (echo), image orientation is determined by the position and direction of the transducer during examination, unlike cardiovascular imaging modalities such as CT or MRI. As a result, when echo images are first shown their display orientation has no external anatomical landmarks, thus the user has to identify anatomical landmarks in the regions of interest to understand the orientation.
Purpose
To display an anatomical model of a standard heart, automatically aligned to an acquired patient’s 3D echo image - assisting image interpretation by quickly orienting the viewer.
Methods
47 echo datasets from 13 pediatric patients with hypoplastic left heart syndrome (HLHS) were annotated by manually indicating the cardiac axes in both ES and ED volumes. We chose a view akin to the standard four chamber view in healthy hearts as the reference view, showing the AV valves, the right atrium, the left atrium and the hypoplastic ventricle. We then trained a deep convolutional neural network (CNN) to predict the rotation required for re-orientation to the reference view. Three data strategies were explored: 1) using 3D images to estimate orientation, 2) using three orthogonal slices only (2.5D approach) and 3) using the central slice only (2D approach). Three different algorithms were investigated: 1) an orientation classifier, 2) an orientation regressor with mean absolute angle error, and 3) an orientation regressor with geodesic loss. The data was split into training, validation and test sets with a 8:1:1 ratio. The training data was augmented by applying random rotations in the range [−10◦, +10◦] and updating labels accordingly. The model with smallest validation error was applied in tandem with the VR visualisation of the echo volumes.
Results
Experimental results suggest that a 2.5D CNN classifying discrete integer angles performs best in re-orienting volumetric images to the reference view, with a mean absolute angle error on the test set of 9.0 deg (test set error ranges from 10.8 to 25.9 deg. for other algorithms). An HLHS volumetric data (left) is automatically aligned with the cardiac model (right) using our trained network when loaded in VR as shown in Figure 1. The volume and the model are both cropped at the referencing plane.
Conclusion
A deep learning network to align 3D echo images to a reference view was successfully trained and then integrated into VR to reorient echo volumes to match a standard anatomical view. This work demonstrates the potential of combining artificial intelligence and VR in medical imaging, although further user study is expected to evaluate its clinical impact.
Caption for Abstract Picture
The VR user interface informs the user of the 3D echo image orientation, automatically aligning it with an anatomical model, here showing the four chamber apical view.
Abstract Figure. Deep learning model integrated into VR
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PD-L1 Expression in Sarcomas: An Immunohistochemical Study. Am J Clin Pathol 2020. [DOI: 10.1093/ajcp/aqaa161.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction/Objective
Immunotherapy is increasingly used for the treatment of metastatic melanoma and carcinomas. PD-I (programmed death 1) and its associated ligand (PD-L1) inhibits the activation of T lymphocytes. This inhibition can be impacted by a number of drugs. Response to these drugs is predicted by assessment of PD-L1 expression. PD-L1 expression varies between 19% and 92% in melanomas and carcinomas. PD-L1 expression is less well documented for sarcomas.
Methods
Fifty-one sarcomas of various histopathologic types were immunohistochemically stained (IHC) for PD-L1 using the antibody clone SP263 (Ventana, Tuscan, AZ). Membrane staining of tumor cells was quantitated as a percentage of total tumor cells. Sarcomas were judged as non-expressors (less than 1%) low-expressors (1 to 50%) and high expressors (greater than 50%). The percentage of each type of sarcoma judged as an expressor was determined.
Results
The percentage of each type of sarcoma expressing PD-L1 is reported and 20% of sarcomas expressed PD- L1. The percentage of sarcomas expressing PD-L1 varied significantly between types but the majority of sarcomas were non-expressors.
Conclusion
PD-L1 IHC expression is valuable in predicting response to immune-modulating drugs. Such therapies may be useful for treatment of metastatic sarcomas. Expression of PD-L1 in carcinomas and melanomas is variable ranging from 19% to 92%. In our study, a minority (20%) of sarcomas expressed PD-L1. Other studies have shown similar results with between 1.4 and 59% (average 24%) of sarcomas expressing PD-L1. Expression appears to be type specific. These finding suggest that PD-L1 based therapy may be less useful in sarcomas than in other malignancies.
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Disseminierte peritoneale Leiomyomatose – Ein Fallbericht. Geburtshilfe Frauenheilkd 2019. [DOI: 10.1055/s-0039-1692099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Viral transmission in honey bees and native bees, supported by a global black queen cell virus phylogeny. Environ Microbiol 2019; 21:972-983. [PMID: 30537211 DOI: 10.1111/1462-2920.14501] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 01/27/2023]
Abstract
In recent decades, we have realized that honey bee viruses are not, in fact, exclusive to honey bees. The potential impact of Apis-affiliated viruses on native pollinators is prompting concern. Our research addresses the issue of virus crossover between honey bees and native bees foraging in the same localities. We measured the presence of black queen cell virus (BQCV), deformed wing virus (DWV) and sacbrood virus (SBV) in managed Apis mellifera (honey bees) and native Andrena spp. (subgenus Melandrena) bee populations in five commercial orchards. We identified viral presence across sites and bees and related these data to measures of bee community diversity. All viruses were found in both managed and native bees, and BQCV was the most common virus in each. To establish evidence for viral crossover between taxa, we undertook an additional examination of BQCV where 74 samples were sequenced and placed in a global phylogenic framework of hundreds of BQCV strains. We demonstrate pathogen sharing across managed honey bees and distantly related wild bees. This phylogenetic analysis contributes to growing evidence for host switching and places local incidence patterns in a worldwide context, revealing multispecies viral transmission.
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Evaluation of 2D and 3D ultrasound tracking algorithms and impact on ultrasound-guided liver radiotherapy margins. Med Phys 2018; 45:4986-5003. [PMID: 30168159 DOI: 10.1002/mp.13152] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Compensation for respiratory motion is important during abdominal cancer treatments. In this work we report the results of the 2015 MICCAI Challenge on Liver Ultrasound Tracking and extend the 2D results to relate them to clinical relevance in form of reducing treatment margins and hence sparing healthy tissues, while maintaining full duty cycle. METHODS We describe methodologies for estimating and temporally predicting respiratory liver motion from continuous ultrasound imaging, used during ultrasound-guided radiation therapy. Furthermore, we investigated the trade-off between tracking accuracy and runtime in combination with temporal prediction strategies and their impact on treatment margins. RESULTS Based on 2D ultrasound sequences from 39 volunteers, a mean tracking accuracy of 0.9 mm was achieved when combining the results from the 4 challenge submissions (1.2 to 3.3 mm). The two submissions for the 3D sequences from 14 volunteers provided mean accuracies of 1.7 and 1.8 mm. In combination with temporal prediction, using the faster (41 vs 228 ms) but less accurate (1.4 vs 0.9 mm) tracking method resulted in substantially reduced treatment margins (70% vs 39%) in contrast to mid-ventilation margins, as it avoided non-linear temporal prediction by keeping the treatment system latency low (150 vs 400 ms). Acceleration of the best tracking method would improve the margin reduction to 75%. CONCLUSIONS Liver motion estimation and prediction during free-breathing from 2D ultrasound images can substantially reduce the in-plane motion uncertainty and hence treatment margins. Employing an accurate tracking method while avoiding non-linear temporal prediction would be favorable. This approach has the potential to shorten treatment time compared to breath-hold and gated approaches, and increase treatment efficiency and safety.
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Abstract
A variety of complications may be experienced during or after endovascular repair (EVAR) of abdominal aortic aneurysms (AAA). Acute procedure-related complications include injury to the access vessels, improper endograft placement, ischaemic and systemic complications as well as the postimplantation syndrome. Femoral pseudoaneurysms, endograft migration, kinking or occlusion, endoleaks and endograft infection are complications that have been observed at follow-up. Meticulous patient selection and preprocedural work-up can reduce the incidence of these complications. The majority of the complications, acute as well those at follow-up, can be dealt with endoluminally. It is of essence, however, that a wide variety of catheters, guidewires, stents, stent-grafts and embolics are readily available in the repertoire of the interventionalist. In a small number of patients with endograft occlusion or infection or with bleeding complications/pseudoaneurysms of the access vessels, open surgical intervention may become necessary. To obtain optimal results, close interdisciplinary co-operation, especially between the interventionist, the vascular surgeon and the anaesthetist is mandatory.
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Sarkomatöse Umwandlung eines aggressiven Angiomyxoms. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1645903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Zervixkarzinom in der Schwangerschaft, Prolongation mittels Chemotherapie. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1645938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Editorial for the special issue of "Computational methods for molecular imaging" for computerized medical imaging and graphics. Comput Med Imaging Graph 2017; 60:1-2. [PMID: 28701281 DOI: 10.1016/j.compmedimag.2017.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sperm whale long-range echolocation sounds revealed by ANTARES, a deep-sea neutrino telescope. Sci Rep 2017; 7:45517. [PMID: 28401960 PMCID: PMC5388847 DOI: 10.1038/srep45517] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/14/2017] [Indexed: 11/09/2022] Open
Abstract
Despite dedicated research has been carried out to adequately map the distribution of the sperm whale in the Mediterranean Sea, unlike other regions of the world, the species population status is still presently uncertain. The analysis of two years of continuous acoustic data provided by the ANTARES neutrino telescope revealed the year-round presence of sperm whales in the Ligurian Sea, probably associated with the availability of cephalopods in the region. The presence of the Ligurian Sea sperm whales was demonstrated through the real-time analysis of audio data streamed from a cabled-to-shore deep-sea observatory that allowed the hourly tracking of their long-range echolocation behaviour on the Internet. Interestingly, the same acoustic analysis indicated that the occurrence of surface shipping noise would apparently not condition the foraging behaviour of the sperm whale in the area, since shipping noise was almost always present when sperm whales were acoustically detected. The continuous presence of the sperm whale in the region confirms the ecological value of the Ligurian sea and the importance of ANTARES to help monitoring its ecosystems.
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Ausgetragene Schwangerschaft nach Endometriumablation mittels Goldnetz. Geburtshilfe Frauenheilkd 2017. [DOI: 10.1055/s-0037-1601506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Der Besondere Fall: Pyoderma Gangränosum im Intervall nach DCIS. Geburtshilfe Frauenheilkd 2017. [DOI: 10.1055/s-0037-1601543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Ungewöhnliche Ursache eines Pelvic Congestion Syndrome – Fallbericht und Literaturrecherche. Geburtshilfe Frauenheilkd 2017. [DOI: 10.1055/s-0037-1601492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Thresholds of toxicological concern – Overview of ongoing scientific developments. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Estimation of toxic hazard – A revised Cramer–Ford–Hall decision tree. Toxicol Lett 2015. [DOI: 10.1016/j.toxlet.2015.08.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Ungewöhnliches Metastasierungsmuster bei mäßig differenziertem endometroiden Corpuskarzinom. Geburtshilfe Frauenheilkd 2015. [DOI: 10.1055/s-0035-1551613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Das fetomaternale Transfusionssyndrom als seltene Ursache nachlassender Kindsbewegungen. Geburtshilfe Frauenheilkd 2015. [DOI: 10.1055/s-0035-1551578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Improving In Vivo High-Resolution CT Imaging of the Tumour Vasculature in Xenograft Mouse Models through Reduction of Motion and Bone-Streak Artefacts. PLoS One 2015; 10:e0128537. [PMID: 26046526 PMCID: PMC4457787 DOI: 10.1371/journal.pone.0128537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/28/2015] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Preclinical in vivo CT is commonly used to visualise vessels at a macroscopic scale. However, it is prone to many artefacts which can degrade the quality of CT images significantly. Although some artefacts can be partially corrected for during image processing, they are best avoided during acquisition. Here, a novel imaging cradle and tumour holder was designed to maximise CT resolution. This approach was used to improve preclinical in vivo imaging of the tumour vasculature. PROCEDURES A custom built cradle containing a tumour holder was developed and fix-mounted to the CT system gantry to avoid artefacts arising from scanner vibrations and out-of-field sample positioning. The tumour holder separated the tumour from bones along the axis of rotation of the CT scanner to avoid bone-streaking. It also kept the tumour stationary and insensitive to respiratory motion. System performance was evaluated in terms of tumour immobilisation and reduction of motion and bone artefacts. Pre- and post-contrast CT followed by sequential DCE-MRI of the tumour vasculature in xenograft transplanted mice was performed to confirm vessel patency and demonstrate the multimodal capacity of the new cradle. Vessel characteristics such as diameter, and branching were quantified. RESULTS Image artefacts originating from bones and out-of-field sample positioning were avoided whilst those resulting from motions were reduced significantly, thereby maximising the resolution that can be achieved with CT imaging in vivo. Tumour vessels ≥ 77 μm could be resolved and blood flow to the tumour remained functional. The diameter of each tumour vessel was determined and plotted as histograms and vessel branching maps were created. Multimodal imaging using this cradle assembly was preserved and demonstrated. CONCLUSIONS The presented imaging workflow minimised image artefacts arising from scanner induced vibrations, respiratory motion and radiopaque structures and enabled in vivo CT imaging and quantitative analysis of the tumour vasculature at higher resolution than was possible before. Moreover, it can be applied in a multimodal setting, therefore combining anatomical and dynamic information.
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Hormontherapie bei adulten Granulosazelltumoren – eine Alternative zur Chemotherapie? Geburtshilfe Frauenheilkd 2014. [DOI: 10.1055/s-0034-1376490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Systemische Methotrexat Therapie bei intramuraler Schwangerschaft – Fallbericht. Geburtshilfe Frauenheilkd 2014. [DOI: 10.1055/s-0034-1376466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Stimulation of endothelial cells with agonistic AT1R autoantibodies leads to upregulation of Angiotensin II receptor 1 (AT1R) and Angiotensin II receptor 2 (AT2R). Thorac Cardiovasc Surg 2013. [DOI: 10.1055/s-0032-1332654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Renoprotective effects of epigallocatechin-3-gallate during cardiopulmonary bypass in a small piglet model. Thorac Cardiovasc Surg 2013. [DOI: 10.1055/s-0032-1332479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Corrigendum to “An evaluation of four automatic methods of segmenting the subcortical structures in the brain” [NeuroImage 47 (2009) 1435–1447]. Neuroimage 2010. [DOI: 10.1016/j.neuroimage.2009.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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An evaluation of four automatic methods of segmenting the subcortical structures in the brain. Neuroimage 2009; 47:1435-47. [PMID: 19463960 DOI: 10.1016/j.neuroimage.2009.05.029] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 05/06/2009] [Accepted: 05/07/2009] [Indexed: 01/02/2023] Open
Abstract
The automation of segmentation of subcortical structures in the brain is an active research area. We have comprehensively evaluated four novel methods of fully automated segmentation of subcortical structures using volumetric, spatial overlap and distance-based measures. Two methods are atlas-based - classifier fusion and labelling (CFL) and expectation-maximisation segmentation using a brain atlas (EMS), and two incorporate statistical models of shape and appearance - profile active appearance models (PAM) and Bayesian appearance models (BAM). Each method was applied to the segmentation of 18 subcortical structures in 270 subjects from a diverse pool varying in age, disease, sex and image acquisition parameters. Our results showed that all four methods perform on par with recently published methods. CFL performed better than the others according to all three classes of metrics. In summary over all structures, the ranking by the Dice coefficient was CFL, BAM, joint EMS and PAM. The Hausdorff distance ranked the methods as CFL, joint PAM and BAM, EMS, whilst percentage absolute volumetric difference ranked them as joint CFL and PAM, joint BAM and EMS. Furthermore, as we had four methods of performing segmentation, we investigated whether the results obtained by each method were more similar to each other than to the manual segmentations using Williams' Index. Reassuringly, the Williams' Index was close to 1 for most subjects (mean=1.02, sd=0.05), indicating better agreement of each method with the gold standard than with the other methods. However, 2% of cases (mainly amygdala and nucleus accumbens) had values outside 3 standard deviations of the mean.
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TU-C-M100J-03: Objective Assessment of Deformable Image Registration in Radiotherapy - a Multi-Institution Study. Med Phys 2007. [DOI: 10.1118/1.2761334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Classical swine fever (CSF) in wild boar: the role of the transplacental infection in the perpetuation of CSF. ACTA ACUST UNITED AC 2005; 52:161-4. [PMID: 16000110 DOI: 10.1111/j.1439-0450.2005.00838.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thirty-four pregnant wild sows and their unborn progeny derived from an endemically infected population in the district of Nordvorpommern (Mecklenburg-Western Pomerania) were investigated for classical swine fever virus (CSFV) and antibodies. During the last 2.5 years of the epidemic, 20 out of 34 pregnant wild sows investigated were serologically positive. No CSFV or viral RNA was detected in organs derived from these animals and their progeny. This indicates that young wild boars persistently infected by transplacental virus transmission do not play a crucial role in the perpetuation of CSFV in wild boar. Other factors seem to be more important for the establishment of CSF as well as for virus perpetuation in the population.
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An inverse problem approach to the estimation of volume change. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2005; 8:616-23. [PMID: 16686011 DOI: 10.1007/11566489_76] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We present a new technique for determining structure-by-structure volume changes, using an inverse problem approach. Given a pre-labelled brain and a series of images at different time-points, we generate finite element meshes from the image data, with volume change modelled by means of an unknown coefficient of expansion on a per-structure basis. We can then determine the volume change in each structure of interest using inverse problem optimization techniques. The proposed method has been tested with simulated and clinical data. Results suggest that the presented technique can be seen as an alternative for volume change estimation.
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Structural basis for pterin antagonism in nitric-oxide synthase. Development of novel 4-oxo-pteridine antagonists of (6R)-5,6,7,8-tetrahydrobiopterin. J Biol Chem 2001; 276:49133-41. [PMID: 11590164 DOI: 10.1074/jbc.m011469200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pathological nitric oxide (NO) generation in sepsis, inflammation, and stroke may be therapeutically controlled by inhibiting NO synthases (NOS). Here we targeted the (6R)-5,6,7,8-tetrahydro-l-biopterin (H(4)Bip)-binding site of NOS, which, upon cofactor binding, maximally increases enzyme activity and NO production from substrate l-arginine. The first generation of H(4)Bip-based NOS inhibitors employed a 4-amino pharmacophore of H(4)Bip analogous to antifolates such as methotrexate. We developed a novel series of 4-oxo-pteridine derivatives that were screened for inhibition against neuronal NOS (NOS-I) and a structure-activity relationship was determined. To understand the structural basis for pterin antagonism, selected derivatives were docked into the NOS pterin binding cavity. Using a reduced 4-oxo-pteridine scaffold, derivatives with certain modifications such as electron-rich aromatic phenyl or benzoyl groups at the 5- and 6-positions, were discovered to markedly inhibit NOS-I, possibly due to hydrophobic and electrostatic interactions with Phe(462) and Ser(104), respectively, within the pterin binding pocket. One of the most effective 4-oxo compounds and, for comparisons an active 4-amino derivative, were then co-crystallized with the endothelial NOS (NOS-III) oxygenase domain and this structure solved to confirm the hypothetical binding modes. Collectively, these findings suggest (i) that, unlike the antifolate principle, the 4-amino substituent is not essential for developing pterin-based NOS inhibitors and (ii), provide a steric and electrostatic basis for their rational design.
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Constructing Patient Specific Models for Correcting Intraoperative Brain Deformation. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION – MICCAI 2001 2001. [DOI: 10.1007/3-540-45468-3_130] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Protein-protein interactions between keratin polypeptides expressed in the yeast two-hybrid system. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1403:158-68. [PMID: 9630597 DOI: 10.1016/s0167-4889(98)00036-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Keratin filaments are obligatory heteropolymers of type I and type II keratin polypeptides. Specific type I/type II pairs are coexpressed in vivo. In contrast, all type I/type II pairs assemble into filaments in vitro, but the different pairs have different stabilities as demonstrated by treatment with increasing concentrations of urea. We have used the yeast two-hybrid system to analyse type I/type II interactions in a cellular context. We measured interactions between two different keratin pairs and we confirm the findings that K6+K17 form very stable heterodimers whereas K8+K18 interactions were weaker. The deletion of head domains did not reduce the strength of type I/type II interactions. Rather, the affinities were increased and the differences between the two pairs were retained in headless mutants. These findings argue against a major role of the head domains in directing heterodimer interactions and in defining heterodimer stabilities.
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Dubious alliance. Am J Health Syst Pharm 1995; 52:1232-3. [PMID: 7656111 DOI: 10.1093/ajhp/52.11.1232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Münchausen's syndrome and medicine men. Lancet 1993; 341:1540. [PMID: 8099416 DOI: 10.1016/0140-6736(93)90682-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Abstract
A single bolus dose of scopolamine (1.0 mg/kg) or saline (equal volume) was injected (i.p.) at 15, 30 or 60 min after fluid percussion traumatic brain injury in the rat. Scopolamine administered at 15 min postinjury significantly reduced beam walking deficits and body weight loss assessed for 5 days after injury. Scopolamine treatment at 30 or 60 min postinjury had no effect on behavioral outcome assessed for 5 days after injury. Plasma concentrations of scopolamine were measured with a radioreceptor assay. The plasma half-life for scopolamine was 21.6 min in injured rats and 17.3 min in normal rats (P less than 0.05). These results, along with evidence from previous studies, suggest that a brief period of excessive neuronal excitation can produce relatively long-lasting behavioral deficits. The temporal effectiveness of receptor antagonist intervention in this process appears to be brief.
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Cholesterol-transfer protein located in the intestinal brush-border membrane. Partial purification and characterization. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1064:275-86. [PMID: 2036443 DOI: 10.1016/0005-2736(91)90312-v] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cholesterol absorption by small intestinal brush border membrane vesicles from taurocholate mixed micelles is a second-order reaction. From a comparison of reaction rates and order before and after proteinase K treatment of brush-border membrane vesicles, it is concluded that cholesterol absorption is protein-mediated. It is shown that the desorption of cholesterol from taurocholate mixed micelles is by a factor of about 10(4) faster than that from egg phosphatidylcholine bilayers. When brush border membrane vesicles are stored at room temperature, intrinsic proteinases are activated and proteins are liberated from the brush border membrane. These proteins collected in the supernatant catalyze cholesterol and phosphatidylcholine exchange between two populations of small unilamellar phospholipid vesicles. One of the active proteins present in the supernatant is purified by a two-step procedure involving gel filtration on Sephadex G-75 SF and affinity chromatography on a Nucleosil-phosphatidylcholine column. The protein thus obtained is pure by polyacrylamide gel electrophoresis in sodium dodecyl sulfate. It has an apparent molecular weight of slightly less than 14,000 as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis and a value of 11,500 determined by gel filtration on Sephadex G-75 SF.
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