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  1. Article ; Online: DinoKnot: Duplex Interaction of Nucleic acids with pseudoKnots.

    Newman, Tara / Chang, Hiu Fung Kevin / Jabbari, Hosna

    IEEE/ACM transactions on computational biology and bioinformatics

    2024  Volume PP

    Abstract: Interaction of nucleic acid molecules is essential for their functional roles in the cell and their applications in biotechnology. While simple duplex interactions have been studied before, the problem of efficiently predicting the minimum free energy ... ...

    Abstract Interaction of nucleic acid molecules is essential for their functional roles in the cell and their applications in biotechnology. While simple duplex interactions have been studied before, the problem of efficiently predicting the minimum free energy structure of more complex interactions with possibly pseudoknotted structures remains a challenge. In this work, we introduce a novel and efficient algorithm for prediction of Duplex Interaction of Nucleic acids with pseudoKnots, DinoKnot follows the hierarchical folding hypothesis to predict the secondary structure of two interacting nucleic acid strands (both homo- and hetero-dimers). DinoKnot utilizes the structure of molecules before interaction as a guide to find their duplex structure allowing for possible base pair competitions. To showcase DinoKnots's capabilities we evaluated its predicted structures against (1) experimental results for SARS-CoV-2 genome and nine primer-probe sets, (2) a clinically verified example of a mutation affecting detection, and (3) a known nucleic acid interaction involving a pseudoknot. In addition, we compared our results against our closest competition, RNAcofold, further highlighting DinoKnot's strengths. We believe DinoKnot can be utilized for various applications including screening new variants for potential detection issues and supporting existing applications involving DNA/RNA interactions, adding structural considerations to the interaction to elicit functional information.
    Language English
    Publishing date 2024-02-12
    Publishing country United States
    Document type Journal Article
    ISSN 1557-9964
    ISSN (online) 1557-9964
    DOI 10.1109/TCBB.2024.3362308
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Strategies and Challenges: Qualitative Lessons Learned From Georgia Produce Prescription Programs.

    Newman, Taylor / Lee, Jung Sun

    Health promotion practice

    2021  Volume 23, Issue 4, Page(s) 699–707

    Abstract: Produce prescription programs (PPPs) have grown in numbers in the past decade, empowering health care providers to promote health by issuing subsidies for produce to vulnerable patients. However, little research has been conducted on the facilitators ... ...

    Abstract Produce prescription programs (PPPs) have grown in numbers in the past decade, empowering health care providers to promote health by issuing subsidies for produce to vulnerable patients. However, little research has been conducted on the facilitators that make it easier for PPPs to succeed or the barriers that programs face, which could provide guidance on how to improve future PPP design and implementation. The study sought to identify the facilitators and barriers affecting positive outcomes in Georgia PPPs called Fruit and Vegetable Prescription (FVRx) Programs. A process evaluation with a qualitative comparative case study approach was conducted. Fifteen FVRx providers, ranging from nutrition educators to farmers market managers, were interviewed in a focus group interview or on the phone between 2016 and 2017. Two nutrition education classes and an FVRx best practices meeting were observed, and program documents were collected. Interview transcripts, field notes from observations, and documents were then thematically analyzed. Four overall themes were determined regarding facilitators and barriers experienced by FVRx programs: (1) creating accessible programming may encourage FVRx participation, (2) provider dedication to the program is important, (3) participants' challenging life circumstances can make participation difficult, and (4) the sustainability of the program is a concern. The findings of this study suggest helpful strategies and challenges for providers to consider when developing and implementing PPPs in Georgia and beyond. Research on the long-term program impact is needed, and policy options for sustainable, scaling up of PPPs should be explored.
    MeSH term(s) Fruit ; Georgia ; Health Promotion ; Humans ; Prescriptions ; Qualitative Research ; Vegetables
    Language English
    Publishing date 2021-08-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2036801-X
    ISSN 1552-6372 ; 1524-8399
    ISSN (online) 1552-6372
    ISSN 1524-8399
    DOI 10.1177/15248399211028558
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  3. Article: Future Time Perspective and Psychological Well-Being for Older Canadian Women During the COVID-19 Pandemic.

    Hytman, Lauren / Hemming, Maya / Newman, Tal / Newton, Nicky J

    Journal of adult development

    2023  , Page(s) 1–11

    Abstract: Relevant literature indicates that one's perception of future time is related to their psychological well-being, particularly for older adults. However, more research is needed to understand this relationship in the context of COVID-19. Older adults may ... ...

    Abstract Relevant literature indicates that one's perception of future time is related to their psychological well-being, particularly for older adults. However, more research is needed to understand this relationship in the context of COVID-19. Older adults may be especially vulnerable to the psychological impacts of the pandemic, but findings on their psychological well-being during COVID-19 are mixed. The current study examines relationships between Future Time Perspective (FTP), COVID-19 impact, and Psychological Well-Being, and how these variables change over 8 months during the earlier period of the pandemic. The current study explored these relationships in a sample of older women in Ontario, Canada, at two time points (
    Language English
    Publishing date 2023-03-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2016657-6
    ISSN 1573-3440 ; 1068-0667
    ISSN (online) 1573-3440
    ISSN 1068-0667
    DOI 10.1007/s10804-023-09445-8
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  4. Article ; Online: Biology is simple.

    Newman, Tim

    Physical biology

    2015  Volume 12, Issue 6, Page(s) 63002

    Abstract: This paper explores the potential for simplicity to reveal new biological understanding. Borrowing selectively from physics thinking, and contrasting with Crick's reductionist philosophy, the author argues that greater emphasis on simplicity is necessary ...

    Abstract This paper explores the potential for simplicity to reveal new biological understanding. Borrowing selectively from physics thinking, and contrasting with Crick's reductionist philosophy, the author argues that greater emphasis on simplicity is necessary to advance biology and its applications.
    MeSH term(s) Biology ; Philosophy ; Physics
    Language English
    Publishing date 2015-12-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2133216-2
    ISSN 1478-3975 ; 1478-3967
    ISSN (online) 1478-3975
    ISSN 1478-3967
    DOI 10.1088/1478-3975/12/6/063002
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  5. Article ; Online: Evidence Suggests a Decrease in the Incidence of Kernicterus in California.

    Walz, Lucas / Brooks, Jordan C / Newman, Thomas

    The Journal of pediatrics

    2022  Volume 255, Page(s) 220–223.e1

    Abstract: We identified children diagnosed with kernicterus in the California Department of Developmental Services and estimated an incidence of 0.42 per 100 000 births from 1988 to 2014, significantly decreasing to 0.04 per 100 000 births after 2009. We also ... ...

    Abstract We identified children diagnosed with kernicterus in the California Department of Developmental Services and estimated an incidence of 0.42 per 100 000 births from 1988 to 2014, significantly decreasing to 0.04 per 100 000 births after 2009. We also examined national infant kernicterus mortality from 1979 to 2016 using CDC data. It did not decrease significantly.
    MeSH term(s) Infant, Newborn ; Infant ; Child ; Humans ; Kernicterus/epidemiology ; Kernicterus/prevention & control ; Jaundice, Neonatal/diagnosis ; Incidence ; California/epidemiology ; Infant Mortality ; Hyperbilirubinemia/complications
    Language English
    Publishing date 2022-12-21
    Publishing country United States
    Document type Case Reports ; Research Support, Non-U.S. Gov't
    ZDB-ID 3102-1
    ISSN 1097-6833 ; 0022-3476
    ISSN (online) 1097-6833
    ISSN 0022-3476
    DOI 10.1016/j.jpeds.2022.11.023
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    In stock of ZB MED Cologne/Königswinter

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  6. Article ; Online: Water is a molecular liquid.

    Newman, Timothy

    Physical biology

    2014  Volume 11, Issue 3, Page(s) 33001

    Abstract: Science and society are failing to grapple with the public health burden of cancer. In this short perspective piece, I contrast reductionism and complexity in cancer research, using water as a simple example, arguing for more 'ecological' approaches to ... ...

    Abstract Science and society are failing to grapple with the public health burden of cancer. In this short perspective piece, I contrast reductionism and complexity in cancer research, using water as a simple example, arguing for more 'ecological' approaches to cancer. This is a call to arms to physical scientists, ecologists and others to get involved, to link up with cancer clinicians and cancer biologists, and an appeal to funding agencies to link up across disciplines to make a difference.
    MeSH term(s) Biomedical Research ; Ecological and Environmental Phenomena ; Humans ; Neoplasm Invasiveness/genetics ; Neoplasm Invasiveness/pathology ; Neoplasms/genetics ; Neoplasms/pathology ; Water/chemistry
    Chemical Substances Water (059QF0KO0R)
    Language English
    Publishing date 2014-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2133216-2
    ISSN 1478-3975 ; 1478-3967
    ISSN (online) 1478-3975
    ISSN 1478-3967
    DOI 10.1088/1478-3975/11/3/033001
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  7. Article ; Online: Author Correction: Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage.

    Newman, Taylor / Krishnan, Laya P / Lee, Jessica / Adami, Guy R

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 2577

    Language English
    Publishing date 2022-02-10
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-06597-7
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  8. Article ; Online: Current Landscape of Produce Prescription Programs in the US.

    Newman, Taylor / Lee, Jung Sun / Thompson, Jennifer Jo / Rajbhandari-Thapa, Janani

    Journal of nutrition education and behavior

    2022  Volume 54, Issue 6, Page(s) 575–581

    Abstract: Objective: To understand the design and implementation models of US produce prescription programs.: Methods: In a mixed-methods study, program providers completed an online survey and an individual phone interview regarding their 2019 programming.: ...

    Abstract Objective: To understand the design and implementation models of US produce prescription programs.
    Methods: In a mixed-methods study, program providers completed an online survey and an individual phone interview regarding their 2019 programming.
    Results: Twenty-three programs completed surveys; 20 completed interviews. Program locations included the mid-Atlantic (26%), Northeast (9%), Midwest (30%), Southwest (17%), and Western regions (17%). Although program models varied, programs generally included a health care visit, usually at a safety-net clinic, and nutrition education, typically counseling, advice, or classes. Prescriptions tended to be farmers market vouchers worth a median of $15 a week (interquartile range, $7.81-$20.00). Transportation was a problem for nearly half of the programs.
    Conclusions and implications: Current produce prescription program characteristics and operations can serve as a blueprint for new and existing programs. Future research should determine program best practices and the opportunity cost between program standardization and local flexibilities.
    MeSH term(s) Farmers ; Fruit ; Health Education/methods ; Humans ; Prescriptions ; Vegetables
    Language English
    Publishing date 2022-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1878-2620
    ISSN (online) 1878-2620
    DOI 10.1016/j.jneb.2022.02.011
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  9. Article: Determining the Association Between the Origin of Sepsis and the Severity of Sepsis in Intensive Care Unit (ICU) Patients Using Acute Physiology and Chronic Health Evaluation (APACHE) IV.

    Arumairaj, Antony J / Habtes, Imnett / Park, Hansang / Valencia-Manrique, Julio C / Arzu, Jennifer / Mattana, Joseph / Chaudhari, Shobhana / Trenard, Natoushka / Newman, Thomas

    Cureus

    2024  Volume 16, Issue 2, Page(s) e54653

    Abstract: Objective The objective of this study is to compare the outcomes of hospital mortality, the requirement of invasive ventilation, vasopressor requirement, duration of vasopressor requirement, and duration of intensive care unit (ICU) stay among the ... ...

    Abstract Objective The objective of this study is to compare the outcomes of hospital mortality, the requirement of invasive ventilation, vasopressor requirement, duration of vasopressor requirement, and duration of intensive care unit (ICU) stay among the different causes of sepsis and to determine which cause of sepsis had the most severe outcomes. Methods A retrospective chart review was done in critically ill adult patients who were admitted with sepsis to the ICU from July 2017 until July 2019. Acute Physiology and Chronic Health Evaluation (APACHE) IV scores were calculated on patients admitted to ICU on day one of ICU admission. Each patient was then evaluated for outcomes of hospital mortality, need for invasive ventilation, requirement of vasopressors, duration of vasopressors, and duration of ICU stay. The outcomes were then compared between the different sources of sepsis to determine which source of sepsis had the highest severity. Results In total, 176 patients were included in the study. Ninety-three patients were admitted with respiratory sepsis, 26 patients were admitted with gastrointestinal sepsis, 31 patients were admitted with urosepsis, and 26 patients were admitted with other miscellaneous causes of sepsis. The hospital mortality was highest in the respiratory sepsis group at 32%, with a trend towards statistical significance with a P value of 0.057. ICU stay duration was highest in patients with respiratory sepsis at six days, with a statistically significant P value of < 0.001. The need for invasive ventilation was highest in patients with respiratory sepsis at 64%, with a statistically significant P value of < 0.001. The requirement of vasopressor support was highest in patients with respiratory sepsis at 47% and the duration of vasopressors was highest in both respiratory and gastrointestinal sepsis at three days, however, there was no statistical significance. Conclusion Among the different origins of sepsis, the patients with respiratory sepsis had the most severe outcomes, with the highest need for invasive ventilation and the highest ICU stay duration.
    Language English
    Publishing date 2024-02-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2747273-5
    ISSN 2168-8184
    ISSN 2168-8184
    DOI 10.7759/cureus.54653
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  10. Article ; Online: Retraction notice to "Impact of the COVID-19 Pandemic on Stroke Epidemiology and Clinical Stroke Practice in the US" [Journal of Stroke and Cerebrovascular Diseases, Vol. 30, No. 4 (April), 2021: 105639].

    Friedlich, Daniel / Newman, Tali / Bricker, Stephanie

    Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association

    2021  Volume 30, Issue 8, Page(s) 105982

    Language English
    Publishing date 2021-07-13
    Publishing country United States
    Document type Retraction of Publication
    ZDB-ID 1131675-5
    ISSN 1532-8511 ; 1052-3057
    ISSN (online) 1532-8511
    ISSN 1052-3057
    DOI 10.1016/j.jstrokecerebrovasdis.2021.105982
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3519: Show issues Location:
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