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  1. Artikel ; Online: A bumpy road ahead for genetic biocontainment.

    George, Dalton R / Danciu, Mark / Davenport, Peter W / Lakin, Matthew R / Chappell, James / Frow, Emma K

    Nature communications

    2024  Band 15, Heft 1, Seite(n) 650

    Sprache Englisch
    Erscheinungsdatum 2024-01-20
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44531-1
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  2. Artikel: Upper respiratory microbial communities of healthy populations are shaped by niche and age.

    Zelasko, Susan / Swaney, Mary Hannah / Sandstrom, Shelby / Davenport, Timothy C / Seroogy, Christine M / Gern, James E / Kalan, Lindsay R / Currie, Cameron R

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Background: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and ... ...

    Abstract Background: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations.
    Results: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.
    Conclusions: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.
    Sprache Englisch
    Erscheinungsdatum 2024-04-14
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.04.14.589416
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  3. Buch ; Online: A Practical Overview of Quantum Computing

    Davenport, James H. / Jones, Jessica R. / Thomason, Matthew

    Is Exascale Possible?

    2023  

    Abstract: Despite numerous advances in the field and a seemingly ever-increasing amount of investment, we are still some years away from seeing a production quantum computer in action. However, it is possible to make some educated guesses about the operational ... ...

    Abstract Despite numerous advances in the field and a seemingly ever-increasing amount of investment, we are still some years away from seeing a production quantum computer in action. However, it is possible to make some educated guesses about the operational difficulties and challenges that may be encountered in practice. We can be reasonably confident that the early machines will be hybrid, with the quantum devices used in an apparently similar way to current accelerators such as FPGAs or GPUs. Compilers, libraries and the other tools relied upon currently for development of software will have to evolve/be reinvented to support the new technology, and training courses will have to be rethought completely rather than ``just'' updated alongside them. The workloads we are likely to see making best use of these hybrid machines will initially be few, before rapidly increasing in diversity as we saw with the uptake of GPUs and other new technologies in the past. This will again be helped by the increase in the number of supporting libraries and development tools, and by the gradual re-development of existing software, to make use of the new quantum devices. Unfortunately, at present the problem of error correction is still largely unsolved, although there have been many advances. Quantum computation is very sensitive to noise, leading to frequent errors during execution. Quantum calculations, although asymptotically faster than their equivalents in ``traditional'' HPC, still take time, and while the profiling tools and programming approaches will have to change drastically, many of the skills honed in the current HPC industry will not suddenly become obsolete, but continue to be useful in the quantum era.

    Comment: 9 pages, 0 figures
    Schlagwörter Computer Science - Distributed ; Parallel ; and Cluster Computing ; Computer Science - Emerging Technologies ; B.m ; B.8.1
    Thema/Rubrik (Code) 028
    Erscheinungsdatum 2023-06-21
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Buch ; Online: The weird and the wonderful in our Solar System

    Rogers, Brian / Lintott, Chris J. / Croft, Steve / Schwamb, Megan E. / Davenport, James R. A.

    Searching for serendipity in the Legacy Survey of Space and Time

    2024  

    Abstract: We present a novel method for anomaly detection in Solar System object data, in preparation for the Legacy Survey of Space and Time. We train a deep autoencoder for anomaly detection and use the learned latent space to search for other interesting ... ...

    Abstract We present a novel method for anomaly detection in Solar System object data, in preparation for the Legacy Survey of Space and Time. We train a deep autoencoder for anomaly detection and use the learned latent space to search for other interesting objects. We demonstrate the efficacy of the autoencoder approach by finding interesting examples, such as interstellar objects, and show that using the autoencoder, further examples of interesting classes can be found. We also investigate the limits of classic unsupervised approaches to anomaly detection through the generation of synthetic anomalies and evaluate the feasibility of using a supervised learning approach. Future work should consider expanding the feature space to increase the variety of anomalies that can be uncovered during the survey using an autoencoder.

    Comment: Accepted by AJ
    Schlagwörter Astrophysics - Earth and Planetary Astrophysics ; Astrophysics - Instrumentation and Methods for Astrophysics ; Computer Science - Machine Learning
    Erscheinungsdatum 2024-01-16
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: A cycle dependent heart - A rare case of menstruation induced neurocardiogenic syncope.

    Azarbal, Jilla R / Vargas, Gustavo A / Davenport, James

    Progress in cardiovascular diseases

    2020  Band 63, Heft 3, Seite(n) 395

    Mesh-Begriff(e) Adult ; Arrhythmias, Cardiac/diagnosis ; Arrhythmias, Cardiac/etiology ; Arrhythmias, Cardiac/physiopathology ; Female ; Heart Rate ; Humans ; Menstruation ; Recurrence ; Syncope, Vasovagal/diagnosis ; Syncope, Vasovagal/etiology ; Syncope, Vasovagal/physiopathology
    Sprache Englisch
    Erscheinungsdatum 2020-03-25
    Erscheinungsland United States
    Dokumenttyp Case Reports ; Letter
    ZDB-ID 209312-1
    ISSN 1873-1740 ; 1532-8643 ; 0033-0620
    ISSN (online) 1873-1740 ; 1532-8643
    ISSN 0033-0620
    DOI 10.1016/j.pcad.2020.03.017
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  6. Artikel ; Online: A Drosophila insulator interacting protein suppresses enhancer-blocking function and modulates replication timing.

    Stow, Emily C / Simmons, James R / An, Ran / Schoborg, Todd A / Davenport, Nastasya M / Labrador, Mariano

    Gene

    2022  Band 819, Seite(n) 146208

    Abstract: Insulators play important roles in genome structure and function in eukaryotes. Interactions between a DNA binding insulator protein and its interacting partner proteins define the properties of each insulator site. The different roles of insulator ... ...

    Abstract Insulators play important roles in genome structure and function in eukaryotes. Interactions between a DNA binding insulator protein and its interacting partner proteins define the properties of each insulator site. The different roles of insulator protein partners in the Drosophila genome and how they confer functional specificity remain poorly understood. The Suppressor of Hairy wing [Su(Hw)] insulator is targeted to the nuclear lamina, preferentially localizes at euchromatin/heterochromatin boundaries, and is associated with the gypsy retrotransposon. Insulator activity relies on the ability of the Su(Hw) protein to bind the DNA at specific sites and interact with Mod(mdg4)67.2 and CP190 partner proteins. HP1 and insulator partner protein 1 (HIPP1) is a partner of Su(Hw), but how HIPP1 contributes to the function of Su(Hw) insulator complexes is unclear. Here, we demonstrate that HIPP1 colocalizes with the Su(Hw) insulator complex in polytene chromatin and in stress-induced insulator bodies. We find that the overexpression of either HIPP1 or Su(Hw) or mutation of the HIPP1 crotonase-like domain (CLD) causes defects in cell proliferation by limiting the progression of DNA replication. We also show that HIPP1 overexpression suppresses the Su(Hw) insulator enhancer-blocking function, while mutation of the HIPP1 CLD does not affect Su(Hw) enhancer blocking. These findings demonstrate a functional relationship between HIPP1 and the Su(Hw) insulator complex and suggest that the CLD, while not involved in enhancer blocking, influences cell cycle progression.
    Mesh-Begriff(e) Animals ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Cell Proliferation ; DNA Replication ; Drosophila/genetics ; Drosophila/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Enhancer Elements, Genetic ; Heterochromatin/metabolism ; Insulator Elements ; Microtubule-Associated Proteins/metabolism ; Mutation ; Nuclear Proteins/metabolism ; Repressor Proteins/genetics ; Repressor Proteins/metabolism
    Chemische Substanzen CP190 protein, Drosophila ; Carrier Proteins ; Drosophila Proteins ; HIPP1 protein, Drosophila ; Heterochromatin ; Microtubule-Associated Proteins ; Nuclear Proteins ; Repressor Proteins ; su(Hw) protein, Drosophila
    Sprache Englisch
    Erscheinungsdatum 2022-01-29
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2022.146208
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  7. Artikel ; Online: Prothrombin complex concentrate (PCC) for treatment of trauma-induced coagulopathy: systematic review and meta-analyses.

    Hannadjas, Ioannis / James, Arthur / Davenport, Ross / Lindsay, Charlotte / Brohi, Karim / Cole, Elaine

    Critical care (London, England)

    2023  Band 27, Heft 1, Seite(n) 422

    Abstract: Background: Trauma-induced coagulopathy (TIC) is common in trauma patients with major hemorrhage. Prothrombin complex concentrate (PCC) is used as a potential treatment for the correction of TIC, but the efficacy, timing, and evidence to support its use ...

    Abstract Background: Trauma-induced coagulopathy (TIC) is common in trauma patients with major hemorrhage. Prothrombin complex concentrate (PCC) is used as a potential treatment for the correction of TIC, but the efficacy, timing, and evidence to support its use in injured patients with hemorrhage are unclear.
    Methods: A systematic search of published studies was performed on MEDLINE and EMBASE databases using standardized search equations. Ongoing studies were identified using clinicaltrials.gov. Studies investigating the use of PCC to treat TIC (on its own or in combination with other treatments) in adult major trauma patients were included. Studies involving pediatric patients, studies of only traumatic brain injury (TBI), and studies involving only anticoagulated patients were excluded. Primary outcomes were in-hospital mortality and venous thromboembolism (VTE). Pooled effects of PCC use were reported using random-effects model meta-analyses. Risk of bias was assessed for each study, and we used the Grading of Recommendations Assessment, Development, and Evaluation to assess the quality of evidence.
    Results: After removing duplicates, 1745 reports were screened and nine observational studies and one randomized controlled trial (RCT) were included, with a total of 1150 patients receiving PCC. Most studies used 4-factor-PCC with a dose of 20-30U/Kg. Among observational studies, co-interventions included whole blood (n = 1), fibrinogen concentrate (n = 2), or fresh frozen plasma (n = 4). Outcomes were inconsistently reported across studies with wide variation in both measurements and time points. The eight observational studies included reported mortality with a pooled odds ratio of 0.97 [95% CI 0.56-1.69], and five reported deep venous thrombosis (DVT) with a pooled OR of 0.83 [95% CI 0.44-1.57]. When pooling the observational studies and the RCT, the OR for mortality and DVT was 0.94 [95% CI 0.60-1.45] and 1.00 [95% CI 0.64-1.55] respectively.
    Conclusions: Among published studies of TIC, PCCs did not significantly reduce mortality, nor did they increase the risk of VTE. However, the potential thrombotic risk remains a concern that should be addressed in future studies. Several RCTs are currently ongoing to further explore the efficacy and safety of PCC.
    Mesh-Begriff(e) Adult ; Humans ; Child ; Venous Thromboembolism ; Blood Coagulation Factors/therapeutic use ; Blood Coagulation Disorders/drug therapy ; Blood Coagulation Disorders/etiology ; Hemorrhage/drug therapy ; Hemorrhage/etiology ; Randomized Controlled Trials as Topic
    Chemische Substanzen prothrombin complex concentrates (37224-63-8) ; Blood Coagulation Factors
    Sprache Englisch
    Erscheinungsdatum 2023-11-02
    Erscheinungsland England
    Dokumenttyp Meta-Analysis ; Systematic Review ; Journal Article
    ZDB-ID 2041406-7
    ISSN 1466-609X ; 1364-8535
    ISSN (online) 1466-609X
    ISSN 1364-8535
    DOI 10.1186/s13054-023-04688-z
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  8. Artikel ; Online: Balancing Statistical Power and Risk in HIV Cure Clinical Trial Design.

    Lau, Jillian S Y / Cromer, Deborah / Pinkevych, Mykola / Lewin, Sharon R / Rasmussen, Thomas A / McMahon, James H / Davenport, Miles P

    The Journal of infectious diseases

    2022  Band 226, Heft 2, Seite(n) 236–245

    Abstract: Background: Analytical treatment interruptions (ATI) are pauses of antiretroviral therapy (ART) in the context of human immunodeficiency virus (HIV) cure trials. They are the gold standard in determining if interventions being tested can achieve ... ...

    Abstract Background: Analytical treatment interruptions (ATI) are pauses of antiretroviral therapy (ART) in the context of human immunodeficiency virus (HIV) cure trials. They are the gold standard in determining if interventions being tested can achieve sustained virological control in the absence of ART. However, withholding ART comes with risks and discomforts to trial participant. We used mathematical models to explore how ATI study design can be improved to maximize statistical power, while minimizing risks to participants.
    Methods: Using previously observed dynamics of time to viral rebound (TVR) post-ATI, we modelled estimates for optimal sample size, frequency, and ATI duration required to detect a significant difference in the TVR between control and intervention groups. Groups were compared using a log-rank test, and analytical and stochastic techniques.
    Results: In placebo-controlled TVR studies, 120 participants are required in each arm to detect 30% difference in frequency of viral reactivation at 80% power. There was little statistical advantage to measuring viral load more frequently than weekly, or interrupting ART beyond 5 weeks in a TVR study.
    Conclusions: Current TVR HIV cure studies are underpowered to detect statistically significant changes in frequency of viral reactivation. Alternate study designs can improve the statistical power of ATI trials.
    Mesh-Begriff(e) Anti-Retroviral Agents/therapeutic use ; Clinical Trials as Topic/methods ; HIV Infections/drug therapy ; Humans ; Research Design ; Risk Assessment ; Viral Load/statistics & numerical data ; Withholding Treatment
    Chemische Substanzen Anti-Retroviral Agents
    Sprache Englisch
    Erscheinungsdatum 2022-02-01
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiac032
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  9. Artikel: Rich Club Characteristics of Alcohol-Naïve Functional Brain Networks Predict Future Drinking Phenotypes in Rhesus Macaques.

    Rowland, Jared A / Stapleton-Kotloski, Jennifer R / Alberto, Greg E / Davenport, April T / Epperly, Phillip M / Godwin, Dwayne W / Daunais, James B

    Frontiers in behavioral neuroscience

    2021  Band 15, Seite(n) 673151

    Abstract: ... ...

    Abstract Purpose
    Sprache Englisch
    Erscheinungsdatum 2021-06-02
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2452960-6
    ISSN 1662-5153
    ISSN 1662-5153
    DOI 10.3389/fnbeh.2021.673151
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  10. Artikel ; Online: Quantifying Y Balance Test performance with multiple and single inertial sensors.

    Johnston, William / Davenport, James / Connelly, Rachelle / Caulfield, Brian

    Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

    2020  Band 2020, Seite(n) 4243–4247

    Abstract: A growing body of evidence has highlighted that inertial sensor data can increase the sensitivity and clinical utility of the Y Balance Test, a commonly used clinical dynamic balance assessment. While early work has demonstrated the value of a single ... ...

    Abstract A growing body of evidence has highlighted that inertial sensor data can increase the sensitivity and clinical utility of the Y Balance Test, a commonly used clinical dynamic balance assessment. While early work has demonstrated the value of a single lumbar worn inertial sensor in quantifying dynamic balance control, no research has investigated if alternative (shank) or combined (lumbar and shank) sensor mounting locations may improve the assessments discriminant capabilities. Determining the optimal sensor set-up is crucial to ensuring minimal cost and maximal utility for clinical users The aim of this cross-sectional study was to investigate if single or multiple inertial sensors, mounted on the lumbar spine and/or shank could differentiate young (18-40 years [n = 41]) and middle-aged (40-65 years [n = 42]) adults, based on dynamic balance performance. Random-forest classification highlighted that a single lumbar sensor could classify age-related differences in performance with an accuracy of 79% (sensitivity = 81%; specificity = 78%). The amalgamation of shank and lumbar data did not significantly improve the classification performance (accuracy = 73-77%; sensitivity = 71-76%; specificity = 73-78%). Jerk magnitude root-mean-square consistently demonstrated predictor importance across the three reach directions: posteromedial (rank 1), anterior (rank 3) and posterolateral (rank 6).
    Mesh-Begriff(e) Cross-Sectional Studies ; Leg ; Lumbar Vertebrae ; Lumbosacral Region ; Physical Therapy Modalities
    Sprache Englisch
    Erscheinungsdatum 2020-08-14
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2694-0604
    ISSN (online) 2694-0604
    DOI 10.1109/EMBC44109.2020.9176416
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