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Article ; Online: (R)-[

Berroterán-Infante, Neydher / Kalina, Thomas / Fetty, Lukas / Janisch, Victoria / Velasco, Ramona / Vraka, Chrysoula / Hacker, Marcus / Haug, Alexander R / Pallitsch, Katharina / Wadsak, Wolfgang / Mitterhauser, Markus

European journal of medicinal chemistry

2019 Volume 176, Page(s) 410–418

Abstract: ... of the established TSPO PET tracer (R)-[ ...

Abstract	Positron emission tomography (PET) imaging of the 18 kDa translocator protein (TSPO), has a high diagnostic potential in neurodegenerative disorders and cancer. However, TSPO is considered a challenge for molecular imaging due to the poor availability of suitable radiotracers with adequate pharmacokinetic properties. Here, we describe the development of a radiofluorinated pyridinyl isoquinoline analogue of the established TSPO PET tracer (R)-[
MeSH term(s)	Animals ; Female ; Fluorine Radioisotopes/chemistry ; Humans ; Isoquinolines/chemical synthesis ; Isoquinolines/chemistry ; Isoquinolines/metabolism ; Isoquinolines/pharmacokinetics ; Isotope Labeling ; Mice, Inbred C57BL ; Microsomes, Liver/metabolism ; Positron-Emission Tomography/methods ; Pyridines/chemical synthesis ; Pyridines/chemistry ; Pyridines/metabolism ; Pyridines/pharmacokinetics ; Radiopharmaceuticals/chemical synthesis ; Radiopharmaceuticals/chemistry ; Radiopharmaceuticals/metabolism ; Radiopharmaceuticals/pharmacokinetics ; Receptors, GABA/metabolism ; Tissue Distribution
Chemical Substances	Bzrp protein, mouse ; Fluorine Radioisotopes ; Isoquinolines ; Pyridines ; Radiopharmaceuticals ; Receptors, GABA ; Fluorine-18 (GZ5I74KB8G)
Language	English
Publishing date	2019-05-10
Publishing country	France
Document type	Journal Article
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2019.05.008
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Article ; Online: Probing the Energy-Smeared R Ratio Using Lattice QCD.

Alexandrou, Constantia / Bacchio, Simone / De Santis, Alessandro / Dimopoulos, Petros / Finkenrath, Jacob / Frezzotti, Roberto / Gagliardi, Giuseppe / Garofalo, Marco / Hadjiyiannakou, Kyriakos / Kostrzewa, Bartosz / Jansen, Karl / Lubicz, Vittorio / Petschlies, Marcus / Sanfilippo, Francesco / Simula, Silvano / Tantalo, Nazario / Urbach, Carsten / Wenger, Urs

Physical review letters

2023 Volume 130, Issue 24, Page(s) 241901

Abstract: We present a first-principles lattice QCD investigation of the R ratio between the e^{+}e^{-} cross ... spectral densities from Euclidean correlators, we compute the R ratio convoluted with Gaussian smearing ... results are compared with the corresponding quantities obtained by smearing the KNT19 compilation [2] of R ...

Abstract	We present a first-principles lattice QCD investigation of the R ratio between the e^{+}e^{-} cross section into hadrons and into muons. By using the method of Ref. [1], that allows one to extract smeared spectral densities from Euclidean correlators, we compute the R ratio convoluted with Gaussian smearing kernels of widths of about 600 MeV and central energies from 220 MeV up to 2.5 GeV. Our theoretical results are compared with the corresponding quantities obtained by smearing the KNT19 compilation [2] of R-ratio experimental measurements with the same kernels and, by centering the Gaussians in the region around the ρ-resonance peak, a tension of about 3 standard deviations is observed. From the phenomenological perspective, we have not included yet in our calculation QED and strong isospin-breaking corrections, and this might affect the observed tension. From the methodological perspective, our calculation demonstrates that it is possible to study the R ratio in Gaussian energy bins on the lattice at the level of accuracy required in order to perform precision tests of the standard model.
MeSH term(s)	Algorithms ; Normal Distribution ; Vibration
Language	English
Publishing date	2023-06-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.130.241901
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Article ; Online: BayesGmed: An R-package for Bayesian causal mediation analysis.

Yimer, Belay B / Lunt, Mark / Beasley, Marcus / Macfarlane, Gary J / McBeth, John

PloS one

2023 Volume 18, Issue 6, Page(s) e0287037

Abstract: ... BayesGmed, an R-package for fitting Bayesian mediation models in R. The application of the methodology (and ... significant. We compared BayesGmed with the mediation R- package, and the results were comparable. Finally ...

Abstract	Background: The past decade has seen an explosion of research in causal mediation analysis. However, most analytic tools developed so far rely on frequentist methods which may not be robust in the case of small sample sizes. In this paper, we propose a Bayesian approach for causal mediation analysis based on Bayesian g-formula, which will overcome the limitations of the frequentist methods. Methods: We created BayesGmed, an R-package for fitting Bayesian mediation models in R. The application of the methodology (and software tool) is demonstrated by a secondary analysis of data collected as part of the MUSICIAN study, a randomised controlled trial of remotely delivered cognitive behavioural therapy (tCBT) for people with chronic pain. We tested the hypothesis that the effect of tCBT would be mediated by improvements in active coping, passive coping, fear of movement and sleep problems. We then demonstrate the use of informative priors to conduct probabilistic sensitivity analysis around violations of causal identification assumptions. Result: The analysis of MUSICIAN data shows that tCBT has better-improved patients' self-perceived change in health status compared to treatment as usual (TAU). The adjusted log-odds of tCBT compared to TAU range from 1.491 (95% CI: 0.452-2.612) when adjusted for sleep problems to 2.264 (95% CI: 1.063-3.610) when adjusted for fear of movement. Higher scores of fear of movement (log-odds, -0.141 [95% CI: -0.245, -0.048]), passive coping (log-odds, -0.217 [95% CI: -0.351, -0.104]), and sleep problem (log-odds, -0.179 [95% CI: -0.291, -0.078]) leads to lower odds of a positive self-perceived change in health status. The result of BayesGmed, however, shows that none of the mediated effects are statistically significant. We compared BayesGmed with the mediation R- package, and the results were comparable. Finally, our sensitivity analysis using the BayesGmed tool shows that the direct and total effect of tCBT persists even for a large departure in the assumption of no unmeasured confounding. Conclusion: This paper comprehensively overviews causal mediation analysis and provides an open-source software package to fit Bayesian causal mediation models.
MeSH term(s)	Humans ; Mediation Analysis ; Bayes Theorem ; Adaptation, Psychological ; Chronic Pain ; Sleep Wake Disorders
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0287037
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Article: Biodistribution and dosimetry of the GluN2B-specific NMDA receptor PET radioligand (R)-[

EJNMMI research

2022 Volume 12, Issue 1, Page(s) 53

Abstract: ... treatment monitoring. Recently, the novel GluN2B-specific PET radioligand (R)-[: Methods: Four healthy ... The GluN2B-specific radioligand (R)-[: Results: Administration of the radioligand was safe without adverse ... The effective dose coefficient was 6.0 µSv/MBq.: Conclusion: The GluN2B-specific radioligand (R)-[ ...

Abstract	Background: The NMDA receptor (NMDAR) plays a key role in the central nervous system, e.g., for synaptic transmission. While synaptic NMDARs are thought to have protective characteristics, activation of extrasynaptic NMDARs might trigger excitotoxic processes linked to neuropsychiatric disorders. Since extrasynaptic NMDARs are typically GluN2B-enriched, the subunit is an interesting target for drug development and treatment monitoring. Recently, the novel GluN2B-specific PET radioligand (R)-[ Methods: Four healthy subjects (two females, two males) underwent one whole-body PET/MR measurement lasting for more than 120 min. The GluN2B-specific radioligand (R)-[ Results: Administration of the radioligand was safe without adverse events. The organs with the highest uptake were the urinary bladder, spleen and pancreas. Organ equivalent dose coefficients were higher in female in almost all organs, except for the urinary bladder of male. The effective dose coefficient was 6.0 µSv/MBq. Conclusion: The GluN2B-specific radioligand (R)-[
Language	English
Publishing date	2022-08-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2619892-7
ISSN	2191-219X
ISSN	2191-219X
DOI	10.1186/s13550-022-00925-8
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Book ; Online: R/V SONNE Cruise SO255 "VITIAZ"

Hauff, Folkmar / Hoernle, Kaj / Gill, Jim / Werner, Reinhard / Timm, Christian / Garbe-Schönberg, Dieter / Gutjahr, Marcus / Jung, Stafan

An integrated major element, trace element and Sr-Nd-Pb-Hf isotope data set of volcanic rocks from the Colville and Kermadec Ridges, the Quaternary Kermadec volcanic front and the Havre Trough backarc basin, Version 1.0

2021

Abstract: Cruise SO255 of the German Research Vessel SONNE surveyed the Kermadec Arc System from ca 35°S to 28°S in 2017. Volcanic rocks were obtained by dredge from the Neogene Colville and Kermadec ridges that represent the split remnants of the preceding Vitiaz ...

Abstract	Cruise SO255 of the German Research Vessel SONNE surveyed the Kermadec Arc System from ca 35°S to 28°S in 2017. Volcanic rocks were obtained by dredge from the Neogene Colville and Kermadec ridges that represent the split remnants of the preceding Vitiaz Arc, the Havre Trough backarc and Quaternary volcanic centers of the Kermadec Arc. The overarching goal of SO255 "VITIAZ" is to elucidate the physical and chemical conditions that control the development of subduction zones, including evolution of mature arc systems, and the transition from arc splitting to back-arc basin generation. The correlated dataset reports major element data for 317 samples, trace element data for 285 samples, radiogenic Sr-Nd-Pb isotope ratios for 155 samples and radiogenic Hf isotope ratios for 88 samples. These include eight topic related samples of cruises TAN0206, TAN1611 of the New Zealand research vessel TANGAROA and one sample of cruise B30 of the Russian research vessel VOLCANOLOG.
Subject code	550
Language	English
Publisher	Interdisciplinary Earth Data Alliance (IEDA)
Publishing country	de
Document type	Book ; Online
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Article ; Online: Historical Perspective: The Career of Dr. R. Nuran Turksoy and the Evolution of Women's Health.

Marcus, Erin N

Journal of women's health (2002)

2023 Volume 32, Issue 9, Page(s) 897–898

MeSH term(s)	Female ; Humans ; Women's Health ; Career Choice
Language	English
Publishing date	2023-06-29
Publishing country	United States
Document type	Editorial
ZDB-ID	1139774-3
ISSN	1931-843X ; 1059-7115 ; 1540-9996
ISSN (online)	1931-843X
ISSN	1059-7115 ; 1540-9996
DOI	10.1089/jwh.2023.0384
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Article ; Online: Genomic Epidemiology and Serology Associated with a SARS-CoV-2 R.1 Variant Outbreak in New Jersey.

Mathema, Barun / Chen, Liang / Wang, Pengfei / Cunningham, Marcus H / Mediavilla, Jose R / Chow, Kar Fai / Luo, Yang / Zhao, Yanan / Composto, Kaelea / Zuckerman, Jerry / Zody, Michael C / Wilson, Nancy / Lee, Annie / Oschwald, Dayna M / Liu, Lihong / Iketani, Sho / Germer, Soren / Fennessey, Samantha / Wang, Maple /

Kramer, Yael / Toole, Patricia / Maniatis, Tom / Ho, David D / Perlin, David S / Kreiswirth, Barry N

mBio

2022 Volume 13, Issue 5, Page(s) e0214122

Abstract: ... on a SARS-CoV-2 nosocomial outbreak caused by the SARS-CoV-2 R.1 variant harboring the E484K mutation ... PCR from 29 October 9 to 30 November 2020. The R.1 variant exhibits partial or complete resistance ... NTD MAbs against pseudovirus harboring single characteristic R.1 mutations highlight the role of S255F ...

Abstract	Examining the neutralizing capacity of monoclonal antibodies (MAbs) used to treat COVID-19, as well as antibodies recovered from unvaccinated, previously vaccinated, and infected individuals, against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) remains critical to study. Here, we report on a SARS-CoV-2 nosocomial outbreak caused by the SARS-CoV-2 R.1 variant harboring the E484K mutation in a 281-bed psychiatric facility in New Jersey among unvaccinated inpatients and health care professionals (HCPs). A total of 81 inpatients and HCPs tested positive for SARS-Cov-2 by reverse transcription (RT)-PCR from 29 October 9 to 30 November 2020. The R.1 variant exhibits partial or complete resistance to two MAbs in clinical use, as well as 2 receptor binding domain MAbs and 4 N-terminal domain (NTD) MAbs. NTD MAbs against pseudovirus harboring single characteristic R.1 mutations highlight the role of S255F in loss of activity. Additionally, we note dampened neutralization capacity by plasma from individuals with previous SARS-CoV-2 infection or sera from vaccinated individuals. The relative resistance of the R.1 variant is likely lower than that of B.1.351 and closer to that of P.1 and B.1.526. The R.1 lineage has been reported in 47 states in the United States and 40 countries. Although high proportions exhibited symptoms (26% and 61% among patients and HCPs, respectively) and relative antibody resistance, we detected only 10 R.1 variants from over 2,900 samples (~0.34%) collected from January to October 2021. Among 3 vaccinated individuals previously infected with R.1, we observed robust neutralizing antibody responses against SARS-CoV-2 wild type and VOCs.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; COVID-19/epidemiology ; Neutralization Tests ; Antibodies, Viral ; New Jersey/epidemiology ; Antibodies, Neutralizing ; Disease Outbreaks ; Antibodies, Monoclonal ; Genomics ; Cross Infection
Chemical Substances	Spike Glycoprotein, Coronavirus ; Antibodies, Viral ; Antibodies, Neutralizing ; Antibodies, Monoclonal
Language	English
Publishing date	2022-08-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.02141-22
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Article ; Online: Hybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus, R. tiliaster, R. glauciformis, R. slesvicensis and R. firmus

Lewin, Marcus / Zhou, Mingyue / Montes, Melanie S. / Mattsson, Tore / Burén, Tomas / Hedrén, Mikael / Ryde, Ulf

Nordic Journal of Botany. 2022 Dec., v. 2022, no. 12 p.e03759-

2022

Abstract: ... are pentaploids and ~8% tetraploids. With MSDA, they are harder to identify than hybrids with R ... idaeus, partly because all Corylifolii species have themselves arisen from R. caesius hybrids and ... therefore share many alleles with R. caesius, partly because hybridisation with R. caesius seems to give rise ...

Abstract	Using flow cytometry and microsatellite DNA analysis (MSDA), we studied hybrids between Rubus caesius and various other Rubus species, with an emphasis on Sweden. We show that hybrids between Rubus caesius and Rubus sect. Corylifolii arise easily. They show a large variation in morphology, but can normally be recognised by a number of characters. They are typically hexaploids, but ~13% of the hybrids are pentaploids and ~8% tetraploids. With MSDA, they are harder to identify than hybrids with R. idaeus, partly because all Corylifolii species have themselves arisen from R. caesius hybrids and therefore share many alleles with R. caesius, partly because hybridisation with R. caesius seems to give rise to some variation in microsatellite regions. Hybrids with species of R. sect. Rubus are much rarer in Sweden and we have only identified one such case. We show that R. cyclomorphus and R. tiliaster are not proper apomictic species, at least not in Sweden, but rather a collection of genetically unrelated hybrids between R. caesius and R. raduloides or R. camptostachys. MSDA analysis of R. slesvicensis and R. firmus shows that these species are problematic. We identify two distinct taxa, one from Skåne in Sweden, which we describe as a new species, R. ruboculus and another from the neighbourhood of Viborg and Schleswig, although the latter is probably not identical with R. slesvicensis s.s. All the other samples form a diverse group of putative R. caesius hybrids at three different ploidy levels. Rubus glauciformis is uniform in Småland, Öland and Blekinge, but becomes harder to distinguish from various hybrids in Skåne. We conclude that once R. caesius and R. idaeus hybrids are properly identified, along with a small number of new apomictic species (often with a local distribution), the genus Rubus does not pose any serious taxonomical problems in Sweden.
Keywords	DNA ; Rubus ; botany ; flow cytometry ; hexaploidy ; hybridization ; microsatellite repeats ; new species ; pentaploidy ; tetraploidy ; Sweden
Language	English
Dates of publication	2022-12
Publishing place	Blackwell Publishing Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2406507-9
ISSN	1756-1051 ; 0107-055X
ISSN (online)	1756-1051
ISSN	0107-055X
DOI	10.1111/njb.03759
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Article ; Online: Keras R-CNN

Jane Hung / Allen Goodman / Deepali Ravel / Stefanie C. P. Lopes / Gabriel W. Rangel / Odailton A. Nery / Benoit Malleret / Francois Nosten / Marcus V. G. Lacerda / Marcelo U. Ferreira / Laurent Rénia / Manoj T. Duraisingh / Fabio T. M. Costa / Matthias Marti / Anne E. Carpenter

BMC Bioinformatics, Vol 21, Iss 1, Pp 1-

library for cell detection in biological images using deep neural networks

2020 Volume 7

Abstract: ... efficiency of biological image analysis. Results We created Keras R-CNN to bring leading computational ... research to the everyday practice of bioimage analysts. Keras R-CNN implements deep learning object ... annotators and find comparable performance. Conclusions Keras R-CNN is a Python package that performs ...

Abstract	Abstract Background A common yet still manual task in basic biology research, high-throughput drug screening and digital pathology is identifying the number, location, and type of individual cells in images. Object detection methods can be useful for identifying individual cells as well as their phenotype in one step. State-of-the-art deep learning for object detection is poised to improve the accuracy and efficiency of biological image analysis. Results We created Keras R-CNN to bring leading computational research to the everyday practice of bioimage analysts. Keras R-CNN implements deep learning object detection techniques using Keras and Tensorflow ( https://github.com/broadinstitute/keras-rcnn ). We demonstrate the command line tool’s simplified Application Programming Interface on two important biological problems, nucleus detection and malaria stage classification, and show its potential for identifying and classifying a large number of cells. For malaria stage classification, we compare results with expert human annotators and find comparable performance. Conclusions Keras R-CNN is a Python package that performs automated cell identification for both brightfield and fluorescence images and can process large image sets. Both the package and image datasets are freely available on GitHub and the Broad Bioimage Benchmark Collection.
Keywords	Deep learning ; Keras ; Convolutional networks ; Malaria ; Object detection ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	004
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Computational Analysis of Histamine Protonation Effects on H 1 R Binding

Marcus Conrad / Anselm H. C. Horn / Heinrich Sticht

Molecules, Vol 28, Iss 3774, p

2023 Volume 3774

Abstract: ... R) has remained elusive. Therefore, we assessed the influence of different histamine tautomers ... dicationic) on the interaction with the ternary histamine-H 1 R-G q complex ... 1 R-G q complex. In addition to the two monocationic tautomers, the binding ...

Abstract	Despite numerous studies investigating histamine and its receptors, the impact of histamine protonation states on binding to the histamine H <semantics> 1 </semantics> -receptor (H <semantics> 1 </semantics> R) has remained elusive. Therefore, we assessed the influence of different histamine tautomers ( <semantics> τ </semantics> -tautomer, <semantics> π </semantics> -tautomer) and charge states (mono- vs. dicationic) on the interaction with the ternary histamine-H <semantics> 1 </semantics> R-G q complex. In atomistic molecular dynamics simulations, the <semantics> τ </semantics> -tautomer formed stable interactions with the receptor, while the <semantics> π </semantics> -tautomer induced a rotation of the histamine ring by 180° and formed only weaker hydrogen bonding interactions. This suggests that the <semantics> τ </semantics> -tautomer is more relevant for stabilization of the active ternary histamine-H <semantics> 1 </semantics> R-G q complex. In addition to the two monocationic tautomers, the binding of dicationic histamine was investigated, whose interaction with the H <semantics> 1 </semantics> R had been observed in a previous experimental study. Our simulations showed that the dication is less compatible with the ternary histamine-H <semantics> 1 </semantics> R-G q complex and rather induces an inactive conformation in the absence of the G q protein. Our data thus indicate that the charge state of histamine critically affects its interactions with the H <semantics> 1 </semantics> R. Ultimately these findings might have implications for the future development of new ligands that stabilize distinct H <semantics> 1 </semantics> R activation states.
Keywords	H 1 R ; histamine ; GPCR ; tautomers ; G q ; protonation ; Organic chemistry ; QD241-441
Subject code	511
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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