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  1. Article ; Online: Response to Ma et al.

    Bergman, David / Lindkvist, Björn / Ludvigsson, Jonas F

    The American journal of gastroenterology

    2024  Volume 119, Issue 1, Page(s) 216–217

    Language English
    Publishing date 2024-02-14
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 390122-1
    ISSN 1572-0241 ; 0002-9270
    ISSN (online) 1572-0241
    ISSN 0002-9270
    DOI 10.14309/ajg.0000000000002543
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Reply.

    Forss, Anders / Bergman, David / Ludvigsson, Jonas F

    Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association

    2023  Volume 22, Issue 3, Page(s) 675–676

    Language English
    Publishing date 2023-10-19
    Publishing country United States
    Document type Letter
    ZDB-ID 2119789-1
    ISSN 1542-7714 ; 1542-3565
    ISSN (online) 1542-7714
    ISSN 1542-3565
    DOI 10.1016/j.cgh.2023.09.037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in

    Chen, Jingxuan / Garfinkel, David J / Bergman, Casey M

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely- ... ...

    Abstract Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely-related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus
    Language English
    Publishing date 2023-12-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.20.572574
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Limited Access to Aortic Valve Procedures in Socioeconomically Disadvantaged Areas.

    David, Guy / Bergman, Alon / Gunnarsson, Candace / Ryan, Michael / Chikermane, Soumya / Thompson, Christin / Clancy, Seth

    Journal of the American Heart Association

    2024  Volume 13, Issue 2, Page(s) e030569

    Abstract: Background: To explore how differences in local socioeconomic deprivation impact access to aortic valve procedures and the treatment of aortic valve disease, in comparison to other open and minimally invasive surgical procedures.: Methods and results!# ...

    Abstract Background: To explore how differences in local socioeconomic deprivation impact access to aortic valve procedures and the treatment of aortic valve disease, in comparison to other open and minimally invasive surgical procedures.
    Methods and results: Procedure volume data were obtained from the Healthcare Cost and Utilization Project from 18 states from 2016 to 2019 and merged with area deprivation index data, an index of zip code-level socioeconomic distress. We estimate the relationship between local deprivation ranking and differences in volumes of aortic valve replacement, which include transcatheter aortic valve replacement (TAVR) and surgical aortic valve replacement (SAVR), versus coronary artery bypass graft surgery and laparoscopic colectomy (LC). All regressions control for state and year fixed effects and an array of zip code-level characteristics. TAVR procedures have increased over time across all zip codes. The rate of increase is negatively correlated with deprivation ranking, regardless of the higher share of hospitalizations per population in high deprivation areas. Distributional analysis further supports these findings, showing that lower area deprivation index areas account for a disproportionately large share of SAVR, TAVR, and LC procedures in our sample relative to their share of all hospitalizations in our sample. By comparison, the cumulative distribution of coronary artery bypass graft procedures was nearly identical to that of total hospitalizations, suggesting that this procedure is equitably distributed. Regressions show high area deprivation index areas have lower prevalence of SAVR (
    Conclusions: People living in high deprivation areas have less access to life-saving technologies, such as SAVR, and even moreso to device-intensive minimally invasive procedures such as TAVR and LC.
    MeSH term(s) Humans ; Aortic Valve/surgery ; Aortic Valve Stenosis/epidemiology ; Aortic Valve Stenosis/surgery ; Heart Valve Prosthesis Implantation/adverse effects ; Heart Valve Prosthesis Implantation/methods ; Treatment Outcome ; Transcatheter Aortic Valve Replacement/adverse effects ; Transcatheter Aortic Valve Replacement/methods ; Risk Factors
    Language English
    Publishing date 2024-01-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2653953-6
    ISSN 2047-9980 ; 2047-9980
    ISSN (online) 2047-9980
    ISSN 2047-9980
    DOI 10.1161/JAHA.123.030569
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Use of different imaging techniques in stab wound analysis.

    Bergman, Linnea / Brock, Fiona / Errickson, David

    Science & justice : journal of the Forensic Science Society

    2023  Volume 64, Issue 1, Page(s) 50–62

    Abstract: Stab wound analysis is a relatively new field of study in forensic science, and there is currently much debate regarding the effectiveness of the analysis due to a lack of validation studies. Furthermore, the underlying viewpoints on the success of stab ... ...

    Abstract Stab wound analysis is a relatively new field of study in forensic science, and there is currently much debate regarding the effectiveness of the analysis due to a lack of validation studies. Furthermore, the underlying viewpoints on the success of stab wound analysis vary. Examination of cut marks, for example, can reveal a variety of characteristics which can be used to determine the type of weapon that was used to inflict them. However, published studies are not consistent when identifying knife blade characteristics, instead considering a wide variety of morphological aspects and their potential value in forensic scenarios. The existing research methodology is therefore inadequate to reliably inform in such contexts, and future experimental design should be influenced by the conditional variance in stabbings in order to provide reliable findings. The research presented here takes a systematic approach to the problem, compiling the published literature (up to September 2023) on the use of different imaging methods applied to stab wound examination to create a taxonomy to examine trends in methodological approaches in both research and investigative settings. This approach identified that published studies could be classified as either morphological or morphometrical, and further sub-classified based on their degree of success and the findings reached. This emphasises the importance of prioritising research into mark data, and the need for a multi-technique, multi-disciplinary approach. A decision tree was created to illustrate which mark attributes should be studied for which purpose, and using which imaging method(s). Furthermore, the research presented identifies two key areas in stab wound research which should be the focus of standardisation efforts, namely methodological procedures and mark characteristic collection. Knife markings are difficult to interpret, but further research and standardisation of kerf mark analysis, as highlighted here, will improve the efficiency and reliability of both forensic investigations and future experimental studies.
    MeSH term(s) Humans ; Reproducibility of Results ; Forensic Sciences ; Research Design ; Wounds, Stab/diagnostic imaging
    Language English
    Publishing date 2023-11-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 1230910-2
    ISSN 1876-4452 ; 1355-0306
    ISSN (online) 1876-4452
    ISSN 1355-0306
    DOI 10.1016/j.scijus.2023.11.002
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  6. Article ; Online: Novel characterization of

    Keller, Nathan A / Bracero, Luis A / Kouba, Insaf / Steinberg, Abigail / Muscat, Jolene / Bergman, David

    Case reports in women's health

    2024  Volume 41, Page(s) e00583

    Abstract: Whole-exome sequencing is an evolving technology in perinatal diagnosis which allows identification of genetic etiologies that would otherwise go undetermined. In this case report, a 38-year-old Hispanic woman, G5P3013, with a monochorionic diamniotic ... ...

    Abstract Whole-exome sequencing is an evolving technology in perinatal diagnosis which allows identification of genetic etiologies that would otherwise go undetermined. In this case report, a 38-year-old Hispanic woman, G5P3013, with a monochorionic diamniotic twin gestation with one fetus displaying significant cranial abnormalities on prenatal ultrasound and magnetic resonance imaging (MRI) of the brain is presented. Fetal anomalies included bilateral ventriculomegaly, absent cavum septum pellucidum, and absent corpus callosum. Diagnostic amniocentesis with chromosome analysis, chromosomal microarray, alpha-fetoprotein, cytomegalovirus, toxoplasmosis, and parvovirus had normal results. Whole-exome sequencing for the anomalous fetus detected a de novo mosaic variant of uncertain significance (VUS) in the calcium/calmodulin dependent serine protein kinase (
    Language English
    Publishing date 2024-01-17
    Publishing country Netherlands
    Document type Case Reports
    ZDB-ID 2800286-6
    ISSN 2214-9112 ; 2214-9112
    ISSN (online) 2214-9112
    ISSN 2214-9112
    DOI 10.1016/j.crwh.2024.e00583
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Pediatric Preventive Care: Population Health and Individualized Care.

    Schor, Edward L / Bergman, David

    Pediatrics

    2021  Volume 148, Issue 3

    Abstract: Well-child care is a near-universal service for young children toward which a great deal of time and professional resources are devoted but for which there is scant evidence of effectiveness in routine practice. It is composed of many components, the ... ...

    Abstract Well-child care is a near-universal service for young children toward which a great deal of time and professional resources are devoted but for which there is scant evidence of effectiveness in routine practice. It is composed of many components, the value of which likely varies with the quality of their provision and the needs and priorities of the children and families who receive them. Achieving more efficient and effective preventive care will require that pediatric practices segment the population they serve and design schedules and staffing to match patients' health, well-being, personal and social circumstances, and service needs. Care should be individualized and include essential screening, tests, procedures, and education on the basis of assessment of patients' and families' needs and priorities. The traditional schedule of individual, comprehensive preventive care visits should be reconsidered and replaced with a schedule that allows complete care to be provided over a series of visits, including those for acute and chronic care. Preventive pediatric care should be provided in family-centered, team-based practices with strong linkages to other providers in the community who serve and support children and families. Care should make use of the wide variety of modalities that exist, and face-to-face time should be reserved for those services that are both important and uniquely responsive to in-office intervention. This model of preventive care will require changes in training, responsibilities and reimbursement of health care team members, and enhanced communication and collaboration among all involved, especially with families.
    MeSH term(s) Child ; Child Health ; Child Health Services/organization & administration ; Health Policy ; Humans ; Parents ; Patient Care Team ; Physician-Patient Relations ; Population Health ; Preventive Health Services/organization & administration ; Quality Assurance, Health Care ; United States
    Language English
    Publishing date 2021-08-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 207677-9
    ISSN 1098-4275 ; 0031-4005
    ISSN (online) 1098-4275
    ISSN 0031-4005
    DOI 10.1542/peds.2020-049877
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Evolution of a Restriction Factor by Domestication of a Yeast Retrotransposon.

    Hannon-Hatfield, J Adam / Chen, Jingxuan / Bergman, Casey M / Garfinkel, David J

    Molecular biology and evolution

    2024  Volume 41, Issue 3

    Abstract: Transposable elements drive genome evolution in all branches of life. Transposable element insertions are often deleterious to their hosts and necessitate evolution of control mechanisms to limit their spread. The long terminal repeat retrotransposon Ty1 ...

    Abstract Transposable elements drive genome evolution in all branches of life. Transposable element insertions are often deleterious to their hosts and necessitate evolution of control mechanisms to limit their spread. The long terminal repeat retrotransposon Ty1 prime (Ty1'), a subfamily of the Ty1 family, is present in many Saccharomyces cerevisiae strains, but little is known about what controls its copy number. Here, we provide evidence that a novel gene from an exapted Ty1' sequence, domesticated restriction of Ty1' relic 2 (DRT2), encodes a restriction factor that inhibits Ty1' movement. DRT2 arose through domestication of a Ty1' GAG gene and contains the C-terminal domain of capsid, which in the related Ty1 canonical subfamily functions as a self-encoded restriction factor. Bioinformatic analysis reveals the widespread nature of DRT2, its evolutionary history, and pronounced structural variation at the Ty1' relic 2 locus. Ty1' retromobility analyses demonstrate DRT2 restriction factor functionality, and northern blot and RNA-seq analysis indicate that DRT2 is transcribed in multiple strains. Velocity cosedimentation profiles indicate an association between Drt2 and Ty1' virus-like particles or assembly complexes. Chimeric Ty1' elements containing DRT2 retain retromobility, suggesting an ancestral role of productive Gag C-terminal domain of capsid functionality is present in the sequence. Unlike Ty1 canonical, Ty1' retromobility increases with copy number, suggesting that C-terminal domain of capsid-based restriction is not limited to the Ty1 canonical subfamily self-encoded restriction factor and drove the endogenization of DRT2. The discovery of an exapted Ty1' restriction factor provides insight into the evolution of the Ty1 family, evolutionary hot-spots, and host-transposable element interactions.
    MeSH term(s) Saccharomyces cerevisiae/genetics ; Retroelements ; Domestication ; DNA Transposable Elements
    Chemical Substances Retroelements ; DNA Transposable Elements
    Language English
    Publishing date 2024-03-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msae050
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Long-Read Genome Assembly of Saccharomyces uvarum Strain CBS 7001.

    Chen, Jingxuan / Garfinkel, David J / Bergman, Casey M

    Microbiology resource announcements

    2022  Volume 11, Issue 1, Page(s) e0097221

    Abstract: Here, we report a long-read genome assembly for Saccharomyces uvarum strain CBS 7001 based on PacBio whole-genome shotgun sequence data. Our assembly provides an improved reference genome for an important yeast in ... ...

    Abstract Here, we report a long-read genome assembly for Saccharomyces uvarum strain CBS 7001 based on PacBio whole-genome shotgun sequence data. Our assembly provides an improved reference genome for an important yeast in the
    Language English
    Publishing date 2022-01-06
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00972-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Cik1 and Vik1 accessory proteins confer distinct functions to the kinesin-14 Kar3.

    Bergman, Zane J / Wong, Jonathan J / Drubin, David G / Barnes, Georjana

    Journal of cell science

    2023  Volume 136, Issue 11

    Abstract: The budding yeast Saccharomyces cerevisiae has a closed mitosis in which the mitotic spindle and the cytoplasmic microtubules (MTs), both of which generate forces to faithfully segregate chromosomes, remain separated by the nuclear envelope throughout ... ...

    Abstract The budding yeast Saccharomyces cerevisiae has a closed mitosis in which the mitotic spindle and the cytoplasmic microtubules (MTs), both of which generate forces to faithfully segregate chromosomes, remain separated by the nuclear envelope throughout the cell cycle. Kar3, the yeast kinesin-14, has distinct functions on MTs in each compartment. Here, we show that two proteins, Cik1 and Vik1, which form heterodimers with Kar3, regulate its localization and function within the cell, and along MTs in a cell cycle-dependent manner. Using a yeast MT dynamics reconstitution assay in lysates from cell cycle-synchronized cells, we found that Kar3-Vik1 induces MT catastrophes in S phase and metaphase, and limits MT polymerization in G1 and anaphase. In contrast, Kar3-Cik1 promotes catastrophes and pauses in G1, while increasing catastrophes in metaphase and anaphase. Adapting this assay to track MT motor protein motility, we observed that Cik1 is necessary for Kar3 to track MT plus-ends in S phase and metaphase but, surprisingly, not during anaphase. These experiments demonstrate how the binding partners of Kar3 modulate its diverse functions both spatially and temporally.
    MeSH term(s) Kinesins/genetics ; Saccharomyces cerevisiae ; Cell Cycle ; Anaphase ; Metaphase
    Chemical Substances Kinesins (EC 3.6.4.4)
    Language English
    Publishing date 2023-06-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    DOI 10.1242/jcs.260621
    Database MEDical Literature Analysis and Retrieval System OnLINE

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