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  1. Book ; Online: Architectural Optimization and Feature Learning for High-Dimensional Time Series Datasets

    Colgan, Robert E. / Yan, Jingkai / Márka, Zsuzsa / Bartos, Imre / Márka, Szabolcs / Wright, John N.

    2022  

    Abstract: As our ability to sense increases, we are experiencing a transition from data-poor problems, in which the central issue is a lack of relevant data, to data-rich problems, in which the central issue is to identify a few relevant features in a sea of ... ...

    Abstract As our ability to sense increases, we are experiencing a transition from data-poor problems, in which the central issue is a lack of relevant data, to data-rich problems, in which the central issue is to identify a few relevant features in a sea of observations. Motivated by applications in gravitational-wave astrophysics, we study the problem of predicting the presence of transient noise artifacts in a gravitational wave detector from a rich collection of measurements from the detector and its environment. We argue that feature learning--in which relevant features are optimized from data--is critical to achieving high accuracy. We introduce models that reduce the error rate by over 60% compared to the previous state of the art, which used fixed, hand-crafted features. Feature learning is useful not only because it improves performance on prediction tasks; the results provide valuable information about patterns associated with phenomena of interest that would otherwise be undiscoverable. In our application, features found to be associated with transient noise provide diagnostic information about its origin and suggest mitigation strategies. Learning in high-dimensional settings is challenging. Through experiments with a variety of architectures, we identify two key factors in successful models: sparsity, for selecting relevant variables within the high-dimensional observations; and depth, which confers flexibility for handling complex interactions and robustness with respect to temporal variations. We illustrate their significance through systematic experiments on real detector data. Our results provide experimental corroboration of common assumptions in the machine-learning community and have direct applicability to improving our ability to sense gravitational waves, as well as to many other problem settings with similarly high-dimensional, noisy, or partly irrelevant data.
    Keywords Computer Science - Machine Learning ; Astrophysics - Instrumentation and Methods for Astrophysics
    Subject code 006
    Publishing date 2022-02-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Boosting the Efficiency of Parametric Detection with Hierarchical Neural Networks

    Yan, Jingkai / Colgan, Robert / Wright, John / Márka, Zsuzsa / Bartos, Imre / Márka, Szabolcs

    2022  

    Abstract: Gravitational wave astronomy is a vibrant field that leverages both classic and modern data processing techniques for the understanding of the universe. Various approaches have been proposed for improving the efficiency of the detection scheme, with ... ...

    Abstract Gravitational wave astronomy is a vibrant field that leverages both classic and modern data processing techniques for the understanding of the universe. Various approaches have been proposed for improving the efficiency of the detection scheme, with hierarchical matched filtering being an important strategy. Meanwhile, deep learning methods have recently demonstrated both consistency with matched filtering methods and remarkable statistical performance. In this work, we propose Hierarchical Detection Network (HDN), a novel approach to efficient detection that combines ideas from hierarchical matching and deep learning. The network is trained using a novel loss function, which encodes simultaneously the goals of statistical accuracy and efficiency. We discuss the source of complexity reduction of the proposed model, and describe a general recipe for initialization with each layer specializing in different regions. We demonstrate the performance of HDN with experiments using open LIGO data and synthetic injections, and observe with two-layer models a $79\%$ efficiency gain compared with matched filtering at an equal error rate of $0.2\%$. Furthermore, we show how training a three-layer HDN initialized using two-layer model can further boost both accuracy and efficiency, highlighting the power of multiple simple layers in efficient detection.
    Keywords Astrophysics - Instrumentation and Methods for Astrophysics ; Computer Science - Machine Learning ; General Relativity and Quantum Cosmology
    Subject code 006
    Publishing date 2022-07-23
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Detecting and Diagnosing Terrestrial Gravitational-Wave Mimics Through Feature Learning

    Colgan, Robert E. / Márka, Zsuzsa / Yan, Jingkai / Bartos, Imre / Wright, John N. / Márka, Szabolcs

    2022  

    Abstract: As engineered systems grow in complexity, there is an increasing need for automatic methods that can detect, diagnose, and even correct transient anomalies that inevitably arise and can be difficult or impossible to diagnose and fix manually. Among the ... ...

    Abstract As engineered systems grow in complexity, there is an increasing need for automatic methods that can detect, diagnose, and even correct transient anomalies that inevitably arise and can be difficult or impossible to diagnose and fix manually. Among the most sensitive and complex systems of our civilization are the detectors that search for incredibly small variations in distance caused by gravitational waves -- phenomena originally predicted by Albert Einstein to emerge and propagate through the universe as the result of collisions between black holes and other massive objects in deep space. The extreme complexity and precision of such detectors causes them to be subject to transient noise issues that can significantly limit their sensitivity and effectiveness. In this work, we present a demonstration of a method that can detect and characterize emergent transient anomalies of such massively complex systems. We illustrate the performance, precision, and adaptability of the automated solution via one of the prevalent issues limiting gravitational-wave discoveries: noise artifacts of terrestrial origin that contaminate gravitational wave observatories' highly sensitive measurements and can obscure or even mimic the faint astrophysical signals for which they are listening. Specifically, we demonstrate how a highly interpretable convolutional classifier can automatically learn to detect transient anomalies from auxiliary detector data without needing to observe the anomalies themselves. We also illustrate several other useful features of the model, including how it performs automatic variable selection to reduce tens of thousands of auxiliary data channels to only a few relevant ones; how it identifies behavioral signatures predictive of anomalies in those channels; and how it can be used to investigate individual anomalies and the channels associated with them.
    Keywords Astrophysics - Instrumentation and Methods for Astrophysics ; Computer Science - Machine Learning ; General Relativity and Quantum Cosmology
    Subject code 006
    Publishing date 2022-03-09
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Mortality and Cardiovascular Outcomes in Adult Non-Liver Solid Organ Transplant Patients With Nonalcoholic Steatohepatitis.

    Dutta, Nirjhar / Marka, Nicholas / Lake, John / Lim, Nicholas

    Transplantation proceedings

    2023  Volume 55, Issue 9, Page(s) 2023–2026

    Abstract: Background: The effect of nonalcoholic steatohepatitis (NASH) on mortality or major adverse cardiovascular events (MACE) in non-liver solid organ transplant recipients (NL-SOT) is unknown.: Methods: Using a retrospective design, adult NL-SOT ... ...

    Abstract Background: The effect of nonalcoholic steatohepatitis (NASH) on mortality or major adverse cardiovascular events (MACE) in non-liver solid organ transplant recipients (NL-SOT) is unknown.
    Methods: Using a retrospective design, adult NL-SOT recipients who had biopsy-proven NASH were compared NL-SOT recipients with normal liver function tests and imaging; propensity matched at a 1:10 ratio on the following: age, sex, race, transplant year, transplant organ, smoking status, and diabetes status. Both deceased and living donor recipients were included; heart and liver transplant patients were excluded. Primary outcome was incidence of all-cause mortality and MACE (a composite outcome of coronary artery disease, ischemic stroke, and peripheral arterial disease).
    Results: Seven patients (3 kidney and 4 lung transplants) had biopsy-proven NASH and 70 patients without NASH, both groups were predominantly male (53%-57%), White (86%-91%), and overweight (mean body mass index ∼ 26). The majority of patients were on calcineurin inhibitors (≥85%), antimetabolites (≥97%), and prednisone (≥50%). Survival analysis showed that NASH patients had a higher risk of death (hazard ratio [HR], 3.24; 95% confidence interval [CI], 1.26-8.33, P = 0.02). NASH did not affect the risk of death-censored graft failure (HR, 1.08; 95% CI, 0.14-8.67; P = .94) or the risk of MACE (HR, 1.03; 95% CI, 0.23-4.62; P = .97).
    Conclusions: In NL-SOT recipients, NASH is significantly associated with mortality but not with MACE.
    MeSH term(s) Humans ; Male ; Adult ; Female ; Non-alcoholic Fatty Liver Disease/complications ; Retrospective Studies ; Organ Transplantation ; Liver Transplantation/adverse effects ; Lung
    Language English
    Publishing date 2023-09-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 82046-5
    ISSN 1873-2623 ; 0041-1345
    ISSN (online) 1873-2623
    ISSN 0041-1345
    DOI 10.1016/j.transproceed.2023.06.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Exploring the birth and death of black holes and other creatures.

    Márka, Szabolcs

    Annals of the New York Academy of Sciences

    2012  Volume 1260, Page(s) 55–65

    Abstract: Astronomers and physicists of diverse interest are teaming up to study enigmatic cosmic phenomena, such as the life cycle of black holes. A "disruptive innovation" is about to emerge during the next decade: Advanced gravitational-wave observatories. The ... ...

    Abstract Astronomers and physicists of diverse interest are teaming up to study enigmatic cosmic phenomena, such as the life cycle of black holes. A "disruptive innovation" is about to emerge during the next decade: Advanced gravitational-wave observatories. The emergence of gravitational-wave physics as a viable observational channel is expected to improve our understanding of the Universe in unprecedented and plausibly unexpected ways, and to enhance the capabilities of the astrophysics community. Detecting cosmic counterparts to gravitational-wave events would revolutionize our understanding of violent astrophysical processes, such as the birth and death of black holes and neutron stars. Although the vanguard of joint observational work with electromagnetic observatories has already rewarded us with a glimpse of the power of gravitational-wave astronomy, the most interesting science is yet to come. Many sources of gravitational-waves are expected to be observable through a broad set of messengers, including γ-rays, X-rays, optical, radio, and neutrino emission. Multimessenger investigations may be crucial for the first detection of gravitational-waves, and could provide the broadest scientific impact afterwards. This paper outlines some exciting aspects of transient multimessenger astronomy with gravitational-waves and highlights open questions that might be resolvable by Advanced or third generation gravitational-wave detector networks. In addition, we will use examples from current research to illustrate that the toolkit of fundamental research can enrich other fields, and that synergistic science can expand horizons here on Earth.
    Language English
    Publishing date 2012-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 211003-9
    ISSN 1749-6632 ; 0077-8923
    ISSN (online) 1749-6632
    ISSN 0077-8923
    DOI 10.1111/j.1749-6632.2011.06414.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: TpopT

    Yan, Jingkai / Wang, Shiyu / Wei, Xinyu Rain / Wang, Jimmy / Márka, Zsuzsanna / Márka, Szabolcs / Wright, John

    Efficient Trainable Template Optimization on Low-Dimensional Manifolds

    2023  

    Abstract: In scientific and engineering scenarios, a recurring task is the detection of low-dimensional families of signals or patterns. A classic family of approaches, exemplified by template matching, aims to cover the search space with a dense template bank. ... ...

    Abstract In scientific and engineering scenarios, a recurring task is the detection of low-dimensional families of signals or patterns. A classic family of approaches, exemplified by template matching, aims to cover the search space with a dense template bank. While simple and highly interpretable, it suffers from poor computational efficiency due to unfavorable scaling in the signal space dimensionality. In this work, we study TpopT (TemPlate OPTimization) as an alternative scalable framework for detecting low-dimensional families of signals which maintains high interpretability. We provide a theoretical analysis of the convergence of Riemannian gradient descent for TpopT, and prove that it has a superior dimension scaling to covering. We also propose a practical TpopT framework for nonparametric signal sets, which incorporates techniques of embedding and kernel interpolation, and is further configurable into a trainable network architecture by unrolled optimization. The proposed trainable TpopT exhibits significantly improved efficiency-accuracy tradeoffs for gravitational wave detection, where matched filtering is currently a method of choice. We further illustrate the general applicability of this approach with experiments on handwritten digit data.
    Keywords Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Signal Processing
    Subject code 006
    Publishing date 2023-10-15
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Book ; Online: Konzeption zur Hospiz- und Palliativarbeit im Freistaat Sachsen

    Ziesch, Marka

    2007  

    Institution Sachsen / Staatsministerium für Soziales
    Author's details Freistaat Sachsen, Staatsministerium für Soziales. [Hrsg.: Sächsisches Staatsministerium für Soziales, Referat Presse- und Öffentlichkeitsarbeit. Red.: Marka Ziesch]
    Language German
    Size 48 S.
    Publishing place Dresden
    Publishing country Germany
    Document type Book ; Online
    HBZ-ID HT015507899
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  8. Book: Gesundheitsfördernde Schule in Sachsen

    Bilz, Ludwig / Ziesch, Marka

    2007  

    Institution Sachsen / Staatsministerium für Soziales
    Author's details Freistaat Sachsen, Staatsministerium für Soziales, Staatsministerium für Kultus. [Hrsg.: Sächsisches Staatsministerium für Soziales, Referat Presse- und Öffentlichkeitsarbeit. Für den Inh. verantw.: Referat Gesundheitsförderung, Gesundheitberichterstattung, Gesunde Ernährung im SMS ... Autoren: Ludwig Bilz ... Red.: Marka Ziesch]
    Subject code 371.374094321
    Language German
    Size 102 S., graph. Darst., 21 cm
    Publisher Zentraler Broschürenversand der Sächsischen Staatsregierung
    Publishing place Dresden
    Publishing country Germany
    Document type Book
    HBZ-ID HT015898784
    Database Catalogue ZB MED Medicine, Health

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  9. Article: Seroprevalence of SARS-CoV-2 IgG in people with cystic fibrosis.

    Mahan, Kathleen / Kiel, Sarah / Freese, Rebecca / Marka, Nicholas / Dunitz, Jordan / Billings, Joanne

    Heliyon

    2024  Volume 10, Issue 6, Page(s) e27567

    Abstract: Background: When the first known US case of COVID-19 (Coronavirus Disease 2019) was reported in early 2020, little was known about the impact of this novel virus on the cystic fibrosis community. As the majority of individuals with CF have chronic lung ... ...

    Abstract Background: When the first known US case of COVID-19 (Coronavirus Disease 2019) was reported in early 2020, little was known about the impact of this novel virus on the cystic fibrosis community. As the majority of individuals with CF have chronic lung disease, this population was initially considered to be at high risk for severe disease as infection with a multitude of viruses has proven to cause pulmonary exacerbation. SARS-CoV-2 virus has proven challenging to study given the multiple disease manifestations, range of severity, and wave-like phenomenon that varies geographically. People with CF who become infected with COVID-19 can be asymptomatic or have symptoms ranging from mild cough and congestion to full respiratory failure, similar to the manifestations seen in non-CF individuals. By studying the seroprevalence, clinical course, and antibody durability due to COVID-19 and vaccinations, we will be better equipped to provide appropriate and informed care to people with CF.
    Methods: Between July 2020 and April 2021 we enrolled 123 people with CF (pwCF) who receive care at the MN CF Center. We monitored their serology every 6 months for SARS-CoV-2 immunoglobulins (nucleocapsid and spike IgG) for evidence of natural and induced immunity. Medication use, pulmonary function, exacerbation history, and hospitalizations were extracted via electronic medical record (EMR).
    Results: 84% (101/120) of enrolled participants were vaccinated against SARS-CoV-2 during the study. Eighty three percent of the cohort showed evidence of either natural or induced "immunity." The average duration of antibody from induced immunity in participants was 6.1 months and from natural immunity was 7.4 months with an overall average duration of antibody of 6.8 months. Earliest antibody detected was 12 days after a single dose of the BNT162b2 vaccine and antibody was detectable across a span of 13 months. Eleven percent of vaccinated individuals did not have measurable IgG. 36% of non-responders (NRs) were solid organ transplant patients on chronic immunosuppressive therapy. Only 3 people within this cohort were hospitalized due to COVID pneumonia and all three survived.
    Conclusion: To our knowledge, this is the first report on the seroprevalence and longevity of SARS-CoV-2 IgG to 1 year in adults with CF after the widespread availability of SARS-CoV-2 vaccinations. These data show that pwCF respond to the COVID vaccination and produce long-lasting antibodies similar to the general population.
    Language English
    Publishing date 2024-03-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2024.e27567
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Body composition after implementation of an enhanced parenteral nutrition protocol in the neonatal intensive care unit: a randomised pilot trial.

    Nagel, Emily M / Super, Jennifer / Marka, Nicholas A / Demerath, Ellen W / Ramel, Sara E

    Annals of human biology

    2024  Volume 51, Issue 1, Page(s) 2306352

    Abstract: Background: Very low birthweight (VLBW) infants are at risk for growth failure and poor neurodevelopment. Optimised parenteral nutrition may help promote optimal growth and development, but concerns that provision of enhanced nutrition may contribute to ...

    Abstract Background: Very low birthweight (VLBW) infants are at risk for growth failure and poor neurodevelopment. Optimised parenteral nutrition may help promote optimal growth and development, but concerns that provision of enhanced nutrition may contribute to increased early adiposity and later metabolic disease remain.
    Aim: To determine associations between provision of an early enhanced parenteral nutrition protocol or standard parenteral nutrition protocol and growth and body composition for VLBW preterm infants in the neonatal intensive care unit.
    Subjects: This is a secondary analysis of data from a clinical trial aimed at assessing the feasibility and safety of randomising VLBW preterm infants to Standard (
    Methods: We evaluated associations between weekly infant growth and body composition measurements from
    Result: No statistically significant associations between nutrition group and infant growth or body composition measures were observed (
    Conclusion: In this pilot trial, enhanced parenteral nutrition in the first week of life was not associated with significant differences in infant growth or body composition during hospitalisation.
    MeSH term(s) Infant ; Infant, Newborn ; Humans ; Infant, Premature ; Pilot Projects ; Intensive Care Units, Neonatal ; Infant, Very Low Birth Weight ; Parenteral Nutrition/methods ; Body Composition ; Randomized Controlled Trials as Topic
    Language English
    Publishing date 2024-01-31
    Publishing country England
    Document type Clinical Trial Protocol ; Journal Article
    ZDB-ID 186656-4
    ISSN 1464-5033 ; 0301-4460
    ISSN (online) 1464-5033
    ISSN 0301-4460
    DOI 10.1080/03014460.2024.2306352
    Database MEDical Literature Analysis and Retrieval System OnLINE

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