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  1. Book ; Online: Combining data assimilation and machine learning to estimate parameters of a convective-scale model

    Legler, Stefanie / Janjic, Tijana

    2021  

    Abstract: Errors in the representation of clouds in convection-permitting numerical weather prediction models can be introduced by different sources. These can be the forcing and boundary conditions, the representation of orography, the accuracy of the numerical ... ...

    Abstract Errors in the representation of clouds in convection-permitting numerical weather prediction models can be introduced by different sources. These can be the forcing and boundary conditions, the representation of orography, the accuracy of the numerical schemes determining the evolution of humidity and temperature, but large contributions are due to the parametrization of microphysics and the parametrization of processes in the surface and boundary layers. These schemes typically contain several tunable parameters that are either not physical or only crudely known, leading to model errors. Traditionally, the numerical values of these model parameters are chosen by manual model tuning. More objectively, they can be estimated from observations by the augmented state approach during the data assimilation. Alternatively, in this work, we look at the problem of parameter estimation through an artificial intelligence lens by training two types of artificial neural networks (ANNs) to estimate several parameters of the one-dimensional modified shallow-water model as a function of the observations or analysis of the atmospheric state. Through perfect model experiments, we show that Bayesian neural networks (BNNs) and Bayesian approximations of point estimate neural networks (NNs) are able to estimate model parameters and their relevant statistics. The estimation of parameters combined with data assimilation for the state decreases the initial state errors even when assimilating sparse and noisy observations. The sensitivity to the number of ensemble members, observation coverage, and neural network size is shown. Additionally, we use the method of layer-wise relevance propagation to gain insight into how the ANNs are learning and discover that they naturally select only a few gridpoints that are subject to strong winds and rain to make their predictions of chosen parameters.
    Keywords Physics - Atmospheric and Oceanic Physics ; Statistics - Machine Learning
    Subject code 612
    Publishing date 2021-09-07
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Understanding the dependence of mean precipitation on convective treatment in tropical aquachannel experiments

    Jung, Hyunju / Knippertz, Peter / Ruckstuhl, Yvonne / Redl, Robert / Janjic, Tijana / Hoose, Corinna

    eISSN: 2698-4016

    2023  

    Abstract: The intertropical convergence zone (ITCZ) is a key circulation and precipitation feature in the tropics. There has been a large spread in the representation of the ITCZ in global weather and climate models for a long time, the reasons for which remain ... ...

    Abstract The intertropical convergence zone (ITCZ) is a key circulation and precipitation feature in the tropics. There has been a large spread in the representation of the ITCZ in global weather and climate models for a long time, the reasons for which remain unclear. This manuscript presents a novel approach with which we disentangle different physical processes responsible for the changeable behavior of the ITCZ in numerical models. The diagnostic tool is based on a conceptual framework developed by Emanuel (2019) and allows for physically consistent estimates of convective mass flux and precipitation efficiency for simulations with explicit and parameterized convection. We apply our diagnostics to a set of tropical aquachannel experiments using the ICOsahedral Nonhydrostatic (ICON) model with horizontal grid resolution of 13 km and with various representations of deep and shallow convection. The channel length corresponds to the Earth's circumference and has rigid walls at 30° N/S. Zonally symmetric sea surface temperatures are prescribed. All four runs share overall similar rainfall patterns and dynamical structures. They simulate an ITCZ at the equator coinciding with the ascending branch of the Hadley circulation, descending branches at 15° N/S with subtropical jets and easterly trade wind belts straddling the ITCZ. Differences are largest between runs with and without parameterized deep convection. With explicit deep convection, rainfall in the ITCZ increases by 35 % and the Hadley circulation as well as surface winds become stronger. Our diagnostic framework reveals that boundary-layer quasi-equilibrium is a key to physically understanding those differences. The stronger surface horizontal winds with explicit deep convection essentially enhance surface enthalpy fluxes and thus perturb quasi-equilibrium in the boundary layer. This is balanced by increasing convective downdraft mass flux that carries low moist static energy from the lower troposphere into the boundary layer. The downdraft strength is proportional ...
    Subject code 551
    Language English
    Publishing date 2023-02-27
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Understanding the dependence of mean precipitation on convective treatment and horizontal resolution in tropical aquachannel experiments

    Jung, Hyunju / Knippertz, Peter / Ruckstuhl, Yvonne / Redl, Robert / Janjic, Tijana / Hoose, Corinna

    eISSN: 2698-4016

    2023  

    Abstract: The Intertropical Convergence Zone (ITCZ) is a key circulation and precipitation feature in the tropics. There has been a large spread in the representation of the ITCZ in global weather and climate models for a long time, the reasons for which remain ... ...

    Abstract The Intertropical Convergence Zone (ITCZ) is a key circulation and precipitation feature in the tropics. There has been a large spread in the representation of the ITCZ in global weather and climate models for a long time, the reasons for which remain unclear. This paper presents a novel approach with which we disentangle different physical processes responsible for the changeable behavior of the ITCZ in numerical models. The diagnostic tool is based on a conceptual framework developed by Emanuel ( 2019 ) and allows for physically consistent estimates of convective mass flux and precipitation efficiency for simulations with explicit and parameterized convection. We apply our diagnostic tool to a set of tropical aquachannel experiments using the ICOsahedral Nonhydrostatic (ICON) model with horizontal grid spacings of 13 and 5 km and with various representations of deep and shallow convection. The channel length corresponds to the Earth's circumference and has rigid walls at 30 ∘ N/S. Zonally symmetric sea surface temperatures are prescribed. All experiments simulate an ITCZ at the Equator coinciding with the ascending branch of the Hadley circulation and descending branches at 15 ∘ N/S with subtropical jets and easterly trade wind belts straddling the ITCZ. With explicit deep convection, however, rainfall in the ITCZ increases and the Hadley circulation becomes stronger. Increasing horizontal resolution substantially reduces the rainfall maximum in the ITCZ, while the strength of the Hadley circulation changes only marginally. Our diagnostic framework reveals that boundary-layer quasi-equilibrium (BLQE) is a key to physically understanding those differences. At 13 km , enhanced surface enthalpy fluxes with explicit deep convection are balanced by increased convective downdrafts. As precipitation efficiency is hardly affected, convective updrafts and rainfall increase. The surface enthalpy fluxes are mainly controlled by mean surface winds, closely linked to the Hadley circulation. These links also help understand ...
    Subject code 551
    Language English
    Publishing date 2023-12-14
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: PD-L1 Expression in Different Segments and Histological Types of Ovarian Cancer According to Lymphocytic Infiltrate.

    Jovanović, Ljubiša / Janković, Radmila / Ćirković, Andja / Jović, Milena / Janjić, Tijana / Djuričić, Slaviša / Milenković, Svetlana

    Medicina (Kaunas, Lithuania)

    2021  Volume 57, Issue 12

    Abstract: Background and ... ...

    Abstract Background and Objectives
    MeSH term(s) B7-H1 Antigen ; Carcinoma, Ovarian Epithelial ; Cystadenocarcinoma, Serous ; Female ; Humans ; Lymphocytes, Tumor-Infiltrating ; Ovarian Neoplasms ; Prognosis
    Chemical Substances B7-H1 Antigen
    Language English
    Publishing date 2021-11-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2188113-3
    ISSN 1648-9144 ; 1010-660X
    ISSN (online) 1648-9144
    ISSN 1010-660X
    DOI 10.3390/medicina57121309
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Prophylactic Low-Dose Paracetamol Administration for Ductal Closure and Microstructural Brain Development in Preterm Infants.

    Sappler, Maria / Hammerl, Marlene / Pellkofer, Yasmin / Griesmaier, Elke / Höck, Michaela / Janjic, Tanja / Gizewski, Elke Ruth / Kiechl-Kohlendorfer, Ursula / Neubauer, Vera

    Neonatology

    2022  Volume 119, Issue 3, Page(s) 361–369

    Abstract: Introduction: Prophylactic low-dose paracetamol administration is used to induce closure of the ductus arteriosus. Effects on the neurological outcome in preterm infants remain unknown. We compared microstructural brain development in very preterm ... ...

    Abstract Introduction: Prophylactic low-dose paracetamol administration is used to induce closure of the ductus arteriosus. Effects on the neurological outcome in preterm infants remain unknown. We compared microstructural brain development in very preterm infants with and without exposure to prophylactic paracetamol by using MR-based diffusion tensor imaging.
    Materials and methods: Infants aged <32 gestational weeks born between October 2014 and December 2018 received prophylactic paracetamol (10 mg/kg intravenously every 8 h until echocardiography after at least 72 h) and form the paracetamol group; infants born between February 2011 and September 2014 form the control group. Fractional anisotropy (FA) and apparent diffusion coefficient (ADC) at term-equivalent age were measured in 14 defined cerebral regions and compared between the groups.
    Results: Included in the study were 340 infants, of whom 217 received prophylactic paracetamol, and 123 formed the control group. The paracetamol group showed significantly higher FA values and lower ADC values in the splenium of the corpus callosum, as well as higher FA values in the pons bilaterally, the left middle cerebellar peduncle, the right occipital white matter, and the right posterior limb of the internal capsule (p ≤ 0.02).
    Conclusion: The perceived safety of prenatal paracetamol exposure has been questioned in recent years. We found no impairment on microstructural maturation processes in the brain of preterm infants at term-equivalent age following early paracetamol administration. The clinical relevance of these imaging findings has to be determined in long-term follow-up studies on neurodevelopmental outcome.
    MeSH term(s) Acetaminophen ; Brain/diagnostic imaging ; Diffusion Tensor Imaging/methods ; Ductus Arteriosus, Patent/diagnostic imaging ; Ductus Arteriosus, Patent/prevention & control ; Female ; Gestational Age ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Pregnancy
    Chemical Substances Acetaminophen (362O9ITL9D)
    Language English
    Publishing date 2022-02-17
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2266911-5
    ISSN 1661-7819 ; 1661-7800
    ISSN (online) 1661-7819
    ISSN 1661-7800
    DOI 10.1159/000521948
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Vagina as a rare location of renal cell carcinoma metastasis.

    Ladjevic, I L / Stefanovic, A / Kadija, S / Terzic, M / Jeremic, K / Janjic, T

    European journal of gynaecological oncology

    2016  Volume 37, Issue 3, Page(s) 434–435

    Abstract: Introduction: Metastatic renal cell carcinoma is often found in distant organs, including lung, bone, brain, and liver. Metastases to the vagina are extremely rare.: Case report: The authors present a case of renal cell carcinoma metastasis to the ... ...

    Abstract Introduction: Metastatic renal cell carcinoma is often found in distant organs, including lung, bone, brain, and liver. Metastases to the vagina are extremely rare.
    Case report: The authors present a case of renal cell carcinoma metastasis to the anterior vaginal wall four months after nephrectomy in a 56-year-old patient. The vaginal lesions were excised. After two years the patient had no signs of recurrence or the disease progression.
    Conclusion: Vaginal metastases should be considered in differential diagnosis of female renal cell carcinoma patients presenting with vaginal bleeding of mass.
    MeSH term(s) Carcinoma, Renal Cell/pathology ; Carcinoma, Renal Cell/secondary ; Female ; Humans ; Kidney Neoplasms/pathology ; Middle Aged ; Vaginal Neoplasms/secondary
    Language English
    Publishing date 2016-06-15
    Publishing country China
    Document type Case Reports ; Journal Article
    ZDB-ID 604589-3
    ISSN 0392-2936
    ISSN 0392-2936
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Feed-forward neural networks using cerebral MR spectroscopy and DTI might predict neurodevelopmental outcome in preterm neonates.

    Janjic, T / Pereverzyev, S / Hammerl, M / Neubauer, V / Lerchner, H / Wallner, V / Steiger, R / Kiechl-Kohlendorfer, U / Zimmermann, M / Buchheim, A / Grams, A E / Gizewski, E R

    European radiology

    2020  Volume 30, Issue 12, Page(s) 6441–6451

    Abstract: Objectives: We aimed to evaluate the ability of feed-forward neural networks (fNNs) to predict the neurodevelopmental outcome (NDO) of very preterm neonates (VPIs) at 12 months corrected age by using biomarkers of cerebral MR proton spectroscopy (: ... ...

    Abstract Objectives: We aimed to evaluate the ability of feed-forward neural networks (fNNs) to predict the neurodevelopmental outcome (NDO) of very preterm neonates (VPIs) at 12 months corrected age by using biomarkers of cerebral MR proton spectroscopy (
    Methods: In this prospective study, 300 VPIs born before 32 gestational weeks received an MRI scan at TEA between September 2013 and December 2017. Due to missing or poor-quality spectroscopy data and missing neurodevelopmental tests, 173 VPIs were excluded. Data sets consisting of 103 and 115 VPIs were considered for prediction of motor and cognitive developmental delay, respectively. Five metabolite ratios and two DTI characteristics in six different areas of the brain were evaluated. A feature selection algorithm was developed for receiving a subset of characteristics prevalent for the VPIs with a developmental delay. Finally, the predictors were constructed employing multiple fNNs and fourfold cross-validation.
    Results: By employing the constructed fNN predictors, we were able to predict cognitive delays of VPIs with 85.7% sensitivity, 100% specificity, 100% positive predictive value (PPV) and 99.1% negative predictive value (NPV). For the prediction of motor delay, we achieved a sensitivity of 76.9%, a specificity of 98.9%, a PPV of 90.9% and an NPV of 96.7%.
    Conclusion: FNNs might be able to predict motor and cognitive development of VPIs at 12 months corrected age when employing biomarkers of cerebral
    Key points: • A feed-forward neuronal network is a promising tool for outcome prediction in premature infants. • Cerebral proton magnetic resonance spectroscopy and diffusion tensor imaging can be used for the construction of early prognostic biomarkers. • Premature infants that would most benefit from early intervention services can be spotted at the time of optimal neuroplasticity.
    MeSH term(s) Brain/diagnostic imaging ; Brain/physiopathology ; Developmental Disabilities/diagnosis ; Developmental Disabilities/physiopathology ; Diffusion Tensor Imaging/methods ; Female ; Humans ; Image Interpretation, Computer-Assisted/methods ; Infant ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/diagnosis ; Infant, Premature, Diseases/physiopathology ; Magnetic Resonance Spectroscopy/methods ; Male ; Neural Networks, Computer ; Predictive Value of Tests ; Prognosis ; Prospective Studies ; Sensitivity and Specificity
    Language English
    Publishing date 2020-07-18
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1085366-2
    ISSN 1432-1084 ; 0938-7994 ; 1613-3749
    ISSN (online) 1432-1084
    ISSN 0938-7994 ; 1613-3749
    DOI 10.1007/s00330-020-07053-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Characteristic facial features and cortical blindness distinguish the DOCK7-related epileptic encephalopathy.

    Haberlandt, Edda / Valovka, Taras / Janjic, Tanja / Müller, Thomas / Blatsios, Georgios / Karall, Daniela / Janecke, Andreas R

    Molecular genetics & genomic medicine

    2021  Volume 9, Issue 3, Page(s) e1607

    Abstract: Background: The epileptic encephalopathies display extensive locus and allelic heterogeneity. Biallelic truncating DOCK7 variants were recently reported in five children with early-onset epilepsy, intellectual disability, and cortical blindness, ... ...

    Abstract Background: The epileptic encephalopathies display extensive locus and allelic heterogeneity. Biallelic truncating DOCK7 variants were recently reported in five children with early-onset epilepsy, intellectual disability, and cortical blindness, indicating that DOCK7 deficiency causes a specific type of epileptic encephalopathy.
    Methods: We identified 23- and 27-year-old siblings with the clinical pattern reported for DOCK7 deficiency, and conducted genome-wide linkage analysis and WES. The consequences of a DOCK7 variant were analyzed on the transcript and protein level in patients' fibroblasts.
    Results: We identified a novel homozygous DOCK7 frameshift variant, an intragenic tandem duplication of 124-kb, previously missed by CGH array, in adult patients. Patients display atrophy in the occipital lobe and pontine hypoplasia with marked pontobulbar sulcus, and focal atrophy of occasional cerebellar folia is a novel finding. Recognizable dysmorphic features include normo-brachycephaly, narrow forehead, low anterior and posterior hairlines, prominent ears, full cheeks, and long eyelashes. Our patients function on the level of 4-year-old children, never showed signs of regression, and seizures are largely controlled with multi-pharmacotherapy. Studies of patients' fibroblasts showed nonsense-mediated RNA decay and lack of DOCK7 protein.
    Conclusion: DOCK7 deficiency causes a definable clinical entity, a recognizable type of epileptic encephalopathy.
    MeSH term(s) Adult ; Blindness, Cortical/genetics ; Blindness, Cortical/pathology ; Cells, Cultured ; Craniofacial Abnormalities/genetics ; Craniofacial Abnormalities/pathology ; Epilepsy/genetics ; Epilepsy/pathology ; Female ; GTPase-Activating Proteins/genetics ; GTPase-Activating Proteins/metabolism ; Guanine Nucleotide Exchange Factors/genetics ; Guanine Nucleotide Exchange Factors/metabolism ; Homozygote ; Humans ; Mutation ; Syndrome
    Chemical Substances DOCK7 protein, human ; GTPase-Activating Proteins ; Guanine Nucleotide Exchange Factors
    Language English
    Publishing date 2021-01-20
    Publishing country United States
    Document type Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2734884-2
    ISSN 2324-9269 ; 2324-9269
    ISSN (online) 2324-9269
    ISSN 2324-9269
    DOI 10.1002/mgg3.1607
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: Impact of combining GRACE and GOCE gravity data on ocean circulation estimates

    Janjić, T. / Schröter, J. / Savcenko, R. / Bosch, W. / Albertella, A. / Rummel, R. / Klatt, O.

    eISSN: 1812-0792

    2018  

    Abstract: With the focus on the Southern Ocean circulation, results of assimilation of multi-mission-altimeter data and the GRACE/GOCE gravity data into the finite element ocean model (FEOM) are investigated. We use the geodetic method to obtain the dynamical ... ...

    Abstract With the focus on the Southern Ocean circulation, results of assimilation of multi-mission-altimeter data and the GRACE/GOCE gravity data into the finite element ocean model (FEOM) are investigated. We use the geodetic method to obtain the dynamical ocean topography (DOT). This method combines the multi-mission-altimeter sea surface height and the GRACE/GOCE gravity field. Using the profile approach, the spectral consistency of both fields is achieved by filtering the sea surface height and the geoid. By combining the GRACE and GOCE data, a considerably shorter filter length can be used, which results in more DOT details. We show that this increase in resolution of measured DOT carries onto the results of data assimilation for the surface data. By assimilating only absolute dynamical topography data using the ensemble Kalman filter, we were able to improve modeled fields. Results are closer to observations which were not used for assimilation and lie outside the area covered by altimetry in the Southern Ocean (e.g. temperature of surface drifters or deep temperatures in the Weddell Sea area at 800 m depth derived from Argo composite.)
    Subject code 551
    Language English
    Publishing date 2018-01-15
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Sequential assimilation of multi-mission dynamical topography into a global finite-element ocean model

    Skachko, S. / Danilov, S. / Janjić, T. / Schröter, J. / Sidorenko, D. / Savcenko, R. / Bosch, W.

    eISSN: 1812-0792

    2018  

    Abstract: This study focuses on an accurate estimation of ocean circulation via assimilation of satellite measurements of ocean dynamical topography into the global finite-element ocean model (FEOM). The dynamical topography data are derived from a complex ... ...

    Abstract This study focuses on an accurate estimation of ocean circulation via assimilation of satellite measurements of ocean dynamical topography into the global finite-element ocean model (FEOM). The dynamical topography data are derived from a complex analysis of multi-mission altimetry data combined with a referenced earth geoid. The assimilation is split into two parts. First, the mean dynamic topography is adjusted. To this end an adiabatic pressure correction method is used which reduces model divergence from the real evolution. Second, a sequential assimilation technique is applied to improve the representation of thermodynamical processes by assimilating the time varying dynamic topography. A method is used according to which the temperature and salinity are updated following the vertical structure of the first baroclinic mode. It is shown that the method leads to a partially successful assimilation approach reducing the rms difference between the model and data from 16 cm to 2 cm. This improvement of the mean state is accompanied by significant improvement of temporal variability in our analysis. However, it remains suboptimal, showing a tendency in the forecast phase of returning toward a free run without data assimilation. Both the mean difference and standard deviation of the difference between the forecast and observation data are reduced as the result of assimilation.
    Subject code 551
    Language English
    Publishing date 2018-01-15
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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