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  1. AU="Elizabeth Sweeney"
  2. AU="Carrigan, M"
  3. AU="Majid T Noghani"
  4. AU="Hanh, Bui Thi Bich"
  5. AU="Hyun Chul Song"
  6. AU="Cottraux, Jean"
  7. AU=Mauro Michael J
  8. AU="Labate, Demetrio"
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  1. Article ; Online: freesurfer

    John Muschelli / Elizabeth Sweeney / Ciprian M. Crainiceanu

    F1000Research, Vol

    Connecting the Freesurfer software with R [version 1; referees: 2 approved]

    2018  Volume 7

    Abstract: We present the package freesurfer, a set of R functions that interface with Freesurfer, a commonly-used open-source software package for processing and analyzing structural neuroimaging data, specifically T1-weighted images. The freesurfer package ... ...

    Abstract We present the package freesurfer, a set of R functions that interface with Freesurfer, a commonly-used open-source software package for processing and analyzing structural neuroimaging data, specifically T1-weighted images. The freesurfer package performs operations on nifti image objects in R using command-line functions from Freesurfer, and returns R objects back to the user. freesurfer allows users to process neuroanatomical images and provides functionality to convert and read the output of the Freesurfer pipelines more easily, including brain images, brain surfaces, and Freesurfer output tables.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2018-05-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Quantifying cognitive resilience in Alzheimer's Disease

    Tianyi Yao / Elizabeth Sweeney / John Nagorski / Joshua M Shulman / Genevera I Allen

    PLoS ONE, Vol 15, Iss 11, p e

    The Alzheimer's Disease Cognitive Resilience Score.

    2020  Volume 0241707

    Abstract: Even though there is a clear link between Alzheimer's Disease (AD) related neuropathology and cognitive decline, numerous studies have observed that healthy cognition can exist in the presence of extensive AD pathology, a phenomenon sometimes called ... ...

    Abstract Even though there is a clear link between Alzheimer's Disease (AD) related neuropathology and cognitive decline, numerous studies have observed that healthy cognition can exist in the presence of extensive AD pathology, a phenomenon sometimes called Cognitive Resilience (CR). To better understand and study CR, we develop the Alzheimer's Disease Cognitive Resilience Score (AD-CR Score), which we define as the difference between the observed and expected cognition given the observed level of AD pathology. Unlike other definitions of CR, our AD-CR Score is a fully non-parametric, stand-alone, individual-level quantification of CR that is derived independently of other factors or proxy variables. Using data from two ongoing, longitudinal cohort studies of aging, the Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP), we validate our AD-CR Score by showing strong associations with known factors related to CR such as baseline and longitudinal cognition, non AD-related pathology, education, personality, APOE, parkinsonism, depression, and life activities. Even though the proposed AD-CR Score cannot be directly calculated during an individual's lifetime because it uses postmortem pathology, we also develop a machine learning framework that achieves promising results in terms of predicting whether an individual will have an extremely high or low AD-CR Score using only measures available during the lifetime. Given this, our AD-CR Score can be used for further investigations into mechanisms of CR, and potentially for subject stratification prior to clinical trials of personalized therapies.
    Keywords Medicine ; R ; Science ; Q
    Subject code 120
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: A suitable time point for quantifying the radiochemical purity of 225Ac-labeled radiopharmaceuticals

    James M. Kelly / Alejandro Amor-Coarasa / Elizabeth Sweeney / Justin J. Wilson / Patrick W. Causey / John W. Babich

    EJNMMI Radiopharmacy and Chemistry, Vol 6, Iss 1, Pp 1-

    2021  Volume 14

    Abstract: Abstract Background As 225Ac-labeled radiopharmaceuticals continue to show promise as targeted alpha therapeutics, there is a growing need to standardize quality control (QC) testing procedures. The determination of radiochemical purity (RCP) is an ... ...

    Abstract Abstract Background As 225Ac-labeled radiopharmaceuticals continue to show promise as targeted alpha therapeutics, there is a growing need to standardize quality control (QC) testing procedures. The determination of radiochemical purity (RCP) is an essential QC test. A significant obstacle to RCP testing is the disruption of the secular equilibrium between actinium-225 and its daughter radionuclides during labeling and QC testing. In order to accelerate translation of actinium-225 targeted alpha therapy, we aimed to determine the earliest time point at which the RCP of an 225Ac-labeled radiopharmaceutical can be accurately quantified. Results Six ligands were conjugated to macrocyclic metal chelators and labeled with actinium-225 under conditions designed to generate diverse incorporation yields. RCP was determined by radio thin layer chromatography (radioTLC) followed by exposure of the TLC plate on a phosphor screen either 0.5, 2, 3.5, 5, 6.5, or 26 h after the plate was developed. The dataset was used to create models for predicting the true RCP for any pre-equilibrium measurement taken at an early time point. The 585 TLC measurements span RCP values of 1.8–99.5%. The statistical model created from these data predicted an independent data set with high accuracy. Predictions made at 0.5 h are more uncertain than predictions made at later time points. This is primarily due to the decay of bismuth-213. A measurement of RCP > 90% at 2 h predicts a true RCP > 97% and guarantees that RCP will exceed 90% after secular equilibrium is reached. These findings were independently validated using NaI(Tl) scintillation counting and high resolution gamma spectroscopy on a smaller set of samples with 10% ≤ RCP ≤ 100%. Conclusions RCP of 225Ac-labeled radiopharmaceuticals can be quantified with acceptable accuracy at least 2 h after radioTLC using various methods of quantifying particle emissions. This time point best balances the need to accurately quantify RCP with the need to safely release the batch as quickly as ...
    Keywords Targeted alpha therapy ; Ac-225 ; Radiopharmacy ; Quality control ; Medical physics. Medical radiology. Nuclear medicine ; R895-920 ; Therapeutics. Pharmacology ; RM1-950
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher SpringerOpen
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Disease correlates of rim lesions on quantitative susceptibility mapping in multiple sclerosis

    Melanie Marcille / Sandra Hurtado Rúa / Charles Tyshkov / Abhishek Jaywant / Joseph Comunale / Ulrike W. Kaunzner / Nancy Nealon / Jai S. Perumal / Lily Zexter / Nicole Zinger / Olivia Bruvik / Yi Wang / Elizabeth Sweeney / Amy Kuceyeski / Thanh D. Nguyen / Susan A. Gauthier

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 10

    Abstract: Abstract Quantitative susceptibility mapping (QSM), an imaging technique sensitive to brain iron, has been used to detect paramagnetic rims of iron-laden active microglia and macrophages in a subset of multiple sclerosis (MS) lesions, known as rim+ ... ...

    Abstract Abstract Quantitative susceptibility mapping (QSM), an imaging technique sensitive to brain iron, has been used to detect paramagnetic rims of iron-laden active microglia and macrophages in a subset of multiple sclerosis (MS) lesions, known as rim+ lesions, that are consistent with chronic active lesions. Because of the potential impact of rim+ lesions on disease progression and tissue damage, investigating their influence on disability and neurodegeneration is critical to establish the impact of these lesions on the disease course. This study aimed to explore the relationship between chronic active rim+ lesions, identified as having a hyperintense rim on QSM, and both clinical disability and imaging measures of neurodegeneration in patients with MS. The patient cohort was composed of 159 relapsing–remitting multiple sclerosis patients. The Expanded Disability Status Scale (EDSS) and Brief International Cognitive Assessment for Multiple Sclerosis, which includes both the Symbol Digit Modalities Test and California Verbal Learning Test-II, were used to assess clinical disability. Cortical thickness and thalamic volume were evaluated as imaging measures of neurodegeneration. A total of 4469 MS lesions were identified, of which 171 QSM rim+ (3.8%) lesions were identified among 57 patients (35.8%). In a multivariate regression model, as the overall total lesion burden increased, patients with at least one rim+ lesion on QSM performed worse on both physical disability and cognitive assessments, specifically the Symbol Digit Modalities Test (p = 0.010), California Verbal Learning Test-II (p = 0.030), and EDSS (p = 0.001). In a separate univariate regression model, controlling for age (p < 0.001) and having at least one rim+ lesion was related to more cortical thinning (p = 0.03) in younger patients (< 45 years). Lower thalamic volume was associated with older patients (p = 0.038) and larger total lesion burden (p < 0.001); however, the association did not remain significant with rim+ lesions (p = 0.10). Our ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 616 ; 610
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Congenic mice confirm that collagen X is required for proper hematopoietic development.

    Elizabeth Sweeney / Douglas Roberts / Tina Corbo / Olena Jacenko

    PLoS ONE, Vol 5, Iss 3, p e

    2010  Volume 9518

    Abstract: The link between endochondral skeletal development and hematopoiesis in the marrow was established in the collagen X transgenic (Tg) and null (KO) mice. Disrupted function of collagen X, a major hypertrophic cartilage matrix protein, resulted in skeletal ...

    Abstract The link between endochondral skeletal development and hematopoiesis in the marrow was established in the collagen X transgenic (Tg) and null (KO) mice. Disrupted function of collagen X, a major hypertrophic cartilage matrix protein, resulted in skeletal and hematopoietic defects in endochondrally derived tissues. Manifestation of the disease phenotype was variable, ranging from perinatal lethality in a subset of mice, to altered lymphopoiesis and impaired immunity in the surviving mice. To exclude contribution of strain specific modifiers to this variable manifestation of the skeleto-hematopoietic phenotype, C57Bl/6 and DBA/2J collagen X congenic lines were established. Comparable disease manifestations confirmed that the skeleto-hematopoietic alterations are an inherent outcome of disrupted collagen X function. Further, colony forming cell assays, complete blood count analysis, serum antibody ELISA, and organ outgrowth studies established altered lymphopoiesis in all collagen X Tg and KO mice and implicated opportunistic infection as a contributor to the severe disease phenotype. These data support a model where endochondral ossification-specific collagen X contributes to the establishment of a hematopoietic niche at the chondro-osseous junction.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2010-03-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Prevention of vaginal SHIV transmission in macaques by a coitally-dependent Truvada regimen.

    Jessica Radzio / Wutyi Aung / Angela Holder / Amy Martin / Elizabeth Sweeney / James Mitchell / Shanon Bachman / Chou-Pong Pau / Walid Heneine / J Gerardo García-Lerma

    PLoS ONE, Vol 7, Iss 12, p e

    2012  Volume 50632

    Abstract: BACKGROUND: Daily pre-exposure prophylaxis (PrEP) with Truvada (a combination of emtricitabine (FTC) and tenofovir (TFV) disoproxil fumarate (TDF)) is a novel HIV prevention strategy recently found to prevent HIV transmission in men who have sex with men ...

    Abstract BACKGROUND: Daily pre-exposure prophylaxis (PrEP) with Truvada (a combination of emtricitabine (FTC) and tenofovir (TFV) disoproxil fumarate (TDF)) is a novel HIV prevention strategy recently found to prevent HIV transmission in men who have sex with men and heterosexual couples. We previously showed that a coitally-dependent Truvada regimen protected macaques against rectal SHIV transmission. Here we examined FTC and tenofovir TFV exposure in vaginal tissues after oral dosing and assessed if peri-coital Truvada also protects macaques against vaginal SHIV infection. METHODS: The pharmacokinetic profile of emtricitabine (FTC) and tenofovir (TFV) was evaluated at first dose. FTC and TFV levels were measured in blood plasma, rectal, and vaginal secretions. Intracellular concentrations of FTC-triphosphate (FTC-TP) and TFV-diphosphate (TFV-DP) were measured in PBMCs, rectal tissues, and vaginal tissues. Efficacy of Truvada in preventing vaginal SHIV infection was assessed using a repeat-exposure vaginal SHIV transmission model consisting of weekly exposures to low doses of SHIV162p3. Six pigtail macaques with normal menstrual cycles received Truvada 24 h before and 2 h after each weekly virus exposure and six received placebo. Infection was monitored by serology and PCR amplification of SHIV RNA and DNA. RESULTS: As in humans, the concentration of FTC was higher than the concentration of TFV in vaginal secretions. Also as in humans, TFV levels in vaginal secretions were lower than in rectal secretions. Intracellular TFV-DP concentrations were also lower in vaginal tissues than in rectal tissues. Despite the low vaginal TFV exposure, all six treated macaques were protected from infection after 18 exposures or 4 full menstrual cycles. In contrast, all 6 control animals were infected. CONCLUSIONS: We modeled a peri-coital regimen with two doses of Truvada and showed that it fully protected macaques from repeated SHIV exposures. Our results open the possibility for simplified PrEP regimens to prevent vaginal HIV ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 630
    Language English
    Publishing date 2012-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure

    Olivier Commowick / Audrey Istace / Michaël Kain / Baptiste Laurent / Florent Leray / Mathieu Simon / Sorina Camarasu Pop / Pascal Girard / Roxana Améli / Jean-Christophe Ferré / Anne Kerbrat / Thomas Tourdias / Frédéric Cervenansky / Tristan Glatard / Jérémy Beaumont / Senan Doyle / Florence Forbes / Jesse Knight / April Khademi /
    Amirreza Mahbod / Chunliang Wang / Richard McKinley / Franca Wagner / John Muschelli / Elizabeth Sweeney / Eloy Roura / Xavier Lladó / Michel M. Santos / Wellington P. Santos / Abel G. Silva-Filho / Xavier Tomas-Fernandez / Hélène Urien / Isabelle Bloch / Sergi Valverde / Mariano Cabezas / Francisco Javier Vera-Olmos / Norberto Malpica / Charles Guttmann / Sandra Vukusic / Gilles Edan / Michel Dojat / Martin Styner / Simon K. Warfield / François Cotton / Christian Barillot

    Scientific Reports, Vol 8, Iss 1, Pp 1-

    2018  Volume 17

    Abstract: Abstract We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent ... ...

    Abstract Abstract We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-theart algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, …), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores.
    Keywords Medicine ; R ; Science ; Q
    Subject code 006
    Language English
    Publishing date 2018-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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