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  1. Article ; Online: The DNA helicase FANCJ (BRIP1) functions in double strand break repair processing, but not crossover formation during prophase I of meiosis in male mice.

    Horan, Tegan S / Ascenção, Carolline F R / Mellor, Christopher / Wang, Meng / Smolka, Marcus B / Cohen, Paula E

    PLoS genetics

    2024  Volume 20, Issue 2, Page(s) e1011175

    Abstract: Meiotic recombination between homologous chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs). Approximately 10% of these DSBs result in crossovers (COs), sites of physical DNA exchange between homologs that are ...

    Abstract Meiotic recombination between homologous chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs). Approximately 10% of these DSBs result in crossovers (COs), sites of physical DNA exchange between homologs that are critical to correct chromosome segregation. Virtually all COs are formed by coordinated efforts of the MSH4/MSH5 and MLH1/MLH3 heterodimers, the latter representing the defining marks of CO sites. The regulation of CO number and position is poorly understood, but undoubtedly requires the coordinated action of multiple repair pathways. In a previous report, we found gene-trap disruption of the DNA helicase, FANCJ (BRIP1/BACH1), elicited elevated numbers of MLH1 foci and chiasmata. In somatic cells, FANCJ interacts with numerous DNA repair proteins including MLH1, and we hypothesized that FANCJ functions with MLH1 to regulate the major CO pathway. To further elucidate the meiotic function of FANCJ, we produced three new Fancj mutant mouse lines via CRISPR/Cas9 gene editing: a full-gene deletion, truncation of the N-terminal Helicase domain, and a C-terminal dual-tagged allele. We also generated an antibody against the C-terminus of the mouse FANCJ protein. Surprisingly, none of our Fancj mutants show any change in either MLH1 focus counts during pachynema or total CO number at diakinesis of prophase I. We find evidence that FANCJ and MLH1 do not interact in meiosis; further, FANCJ does not co-localize with MSH4, MLH1, or MLH3 in meiosis. Instead, FANCJ co-localizes with BRCA1 and TOPBP1, forming discrete foci along the chromosome cores beginning in early meiotic prophase I and densely localized to unsynapsed chromosome axes in late zygonema and to the XY chromosomes in early pachynema. Fancj mutants also exhibit a subtle persistence of DSBs in pachynema. Collectively, these data indicate a role for FANCJ in early DSB repair, but they rule out a role for FANCJ in MLH1-mediated CO events.
    MeSH term(s) Animals ; Male ; Mice ; Alleles ; DNA Helicases/genetics ; DNA Repair/genetics ; Meiosis/genetics ; Meiotic Prophase I/genetics
    Chemical Substances DNA Helicases (EC 3.6.4.-) ; Brip1 protein, mouse (EC 3.6.4.13)
    Language English
    Publishing date 2024-02-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1011175
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: The DNA helicase FANCJ (BRIP1) functions in Double Strand Break repair processing, but not crossover formation during Prophase I of meiosis in male mice.

    Horan, Tegan S / Ascenção, Carolline F R / Mellor, Christopher A / Wang, Meng / Smolka, Marcus B / Cohen, Paula E

    bioRxiv : the preprint server for biology

    2023  

    Abstract: During meiotic prophase I, recombination between homologous parental chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs), each of which must be repaired with absolute fidelity to ensure genome stability of the ... ...

    Abstract During meiotic prophase I, recombination between homologous parental chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs), each of which must be repaired with absolute fidelity to ensure genome stability of the germline. One outcome of these DSB events is the formation of Crossovers (COs), the sites of physical DNA exchange between homologs that are critical to ensure the correct segregation of parental chromosomes. However, COs account for only a small (~10%) proportion of all DSB repair events; the remaining 90% are repaired as non-crossovers (NCOs), most by synthesis dependent strand annealing. Virtually all COs are formed by coordinated efforts of the MSH4/MSH5 and MLH1/MLH3 heterodimers. The number and positioning of COs is exquisitely controlled via mechanisms that remain poorly understood, but which undoubtedly require the coordinated action of multiple repair pathways downstream of the initiating DSB. In a previous report we found evidence suggesting that the DNA helicase and Fanconi Anemia repair protein, FANCJ (BRIP1/BACH1), functions to regulate meiotic recombination in mouse. A gene-trap disruption of
    Language English
    Publishing date 2023-10-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.06.561296
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Predictors of Stone-Related Events in Asymptomatic Untreated Intrarenal Calculi.

    Daly, Killian F / Horan, Michelle T / Lincoln, Marc C / MacCraith, Eoin / Quinlan, Mark R / Walsh, Michael T / Skolarikos, Andreas / Davis, Niall F

    Journal of endourology

    2022  Volume 36, Issue 4, Page(s) 444–447

    Abstract: Purpose: ...

    Abstract Purpose:
    MeSH term(s) Female ; Humans ; Kidney ; Kidney Calculi/complications ; Male ; Renal Colic/etiology ; Retrospective Studies ; Tomography, X-Ray Computed/adverse effects ; Ureter ; Ureteral Calculi/complications
    Language English
    Publishing date 2022-01-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 356931-7
    ISSN 1557-900X ; 0892-7790
    ISSN (online) 1557-900X
    ISSN 0892-7790
    DOI 10.1089/end.2021.0736
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Predicting male dairy calf live weight for use in calf management decision support.

    Dunne, F L / Kelleher, M M / Horan, B / Evans, R D / Berry, D P

    JDS communications

    2021  Volume 2, Issue 5, Page(s) 257–261

    Abstract: The growing awareness and scrutiny of the management of young dairy calves, especially male calves, necessitates a support tool to aid in the planning of resource allocation on dairy farms. There is a desire among some vendors for a minimum calf weight ... ...

    Abstract The growing awareness and scrutiny of the management of young dairy calves, especially male calves, necessitates a support tool to aid in the planning of resource allocation on dairy farms. There is a desire among some vendors for a minimum calf weight when purchasing young dairy bull calves. Hence, the objective of the present study was to investigate whether live weight of young calves (approximately 10-50 d old) can be predicted using readily accessible animal-level features, especially features that may be available in advance of birth. A multiple linear regression mixed model was developed with the live weight of 602 dairy bull calves aged between 10 and 42 d as the dependent variable; the age at which an animal is predicted to reach a predefined live weight was then estimated based on the model regression coefficients. Fixed effects included in the multiple regression model were dam parity, gestation length, and parental average genetic merit for relevant traits available in Ireland; namely, birth weight, birth size, and carcass weight. Herd of origin was included as a random effect, with all calves having been sold directly from the farm of birth. Live weight data were recorded at the point of sale when calves were, on average, 26 d old with a mean live weight of 56.6 kg. Animals were randomly assigned to 10 separate (i.e., folds) cross-validation data sets without replacement (i.e., each fold consisted of a different 10% of the data to test the model, with the remaining 90% of data being used to train the model) to quantify the accuracy of prediction. Across all data, the correlation between actual and predicted live weight was 0.76; the regression coefficient of actual live weight on predicted live weight across all data was 0.99. The root mean squared error of prediction varied from 4.40 to 6.66 kg per fold. Across all data, the root mean squared error was 5.61 kg, implying that 68% of live weight predictions were within 5.61 kg of the actual live weight. Given the potential availability of all model features in advance of birth (gestation length can be predicted from ultrasound examination of the pregnant uterus, although substituting parental average genetic merit for gestation length had minimal effect on model performance), predictions can be integrated into a dairy farm decision support tool to aid in the management of labor and infrastructure resources to achieve minimum live weight specifications before sale.
    Language English
    Publishing date 2021-07-01
    Publishing country United States
    Document type Journal Article
    ISSN 2666-9102
    ISSN (online) 2666-9102
    DOI 10.3168/jdsc.2021-0078
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Validating inborn error of immunity prevalence and risk with nationally representative electronic health record data.

    Rider, Nicholas L / Truxton, Ahuva / Ohrt, Tracy / Margolin-Katz, Irene / Horan, Mary / Shin, Harold / Davila, Roger / Tenembaum, Vanessa / Quinn, Jessica / Modell, Vicki / Modell, Fred / Orange, Jordan S / Branner, Almut / Senerchia, Cynthia

    The Journal of allergy and clinical immunology

    2024  

    Abstract: Background: The 10 Warning Signs of Primary Immunodeficiency were created 30 years ago to advance recognition of inborn errors of immunity (IEI). However, no population-level assessment of their utility applied to electronic health record (EHR) data has ...

    Abstract Background: The 10 Warning Signs of Primary Immunodeficiency were created 30 years ago to advance recognition of inborn errors of immunity (IEI). However, no population-level assessment of their utility applied to electronic health record (EHR) data has been conducted.
    Objective: We sought to quantify the value of having ≥2 warning signs (WS) toward diagnosing IEI using a highly representative real-world US cohort. A secondary goal was estimating the US prevalence of IEI.
    Methods: In this cohort study, we accessed normalized and de-identified EHR data on 152 million US patients. An IEI cohort (n = 41,080), in which patients were defined by having at least 1 verifiable IEI diagnosis placed ≥2 times in their record, was compared with a matched set of controls (n = 250,262). WS were encoded along with relevant diagnoses, relative weights were calculated, and the proportion of IEI cases versus controls with ≥2 WS was compared.
    Results: The proportion of IEI cases with ≥2 WS significantly differed from controls (0.33 vs 0.031; P < .0005, χ
    Conclusions: This nationally representative US-based cohort study demonstrates that presence of WS and associated clinical diagnoses can facilitate identification of patients with IEI from EHR data. In addition, we estimate that 6 in 10,000, or approximately 150,000 to 200,000 individuals are affected by IEI across the United States.
    Language English
    Publishing date 2024-01-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 121011-7
    ISSN 1097-6825 ; 1085-8725 ; 0091-6749
    ISSN (online) 1097-6825 ; 1085-8725
    ISSN 0091-6749
    DOI 10.1016/j.jaci.2024.01.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Single cell cortical bone transcriptomics define novel osteolineage gene sets altered in chronic kidney disease.

    Agoro, Rafiou / Nookaew, Intawat / Noonan, Megan L / Marambio, Yamil G / Liu, Sheng / Chang, Wennan / Gao, Hongyu / Hibbard, Lainey M / Metzger, Corinne E / Horan, Daniel / Thompson, William R / Xuei, Xiaoling / Liu, Yunlong / Zhang, Chi / Robling, Alexander G / Bonewald, Lynda F / Wan, Jun / White, Kenneth E

    Frontiers in endocrinology

    2023  Volume 14, Page(s) 1063083

    Abstract: Introduction: Due to a lack of spatial-temporal resolution at the single cell level, the etiologies of the bone dysfunction caused by diseases such as normal aging, osteoporosis, and the metabolic bone disease associated with chronic kidney disease (CKD) ...

    Abstract Introduction: Due to a lack of spatial-temporal resolution at the single cell level, the etiologies of the bone dysfunction caused by diseases such as normal aging, osteoporosis, and the metabolic bone disease associated with chronic kidney disease (CKD) remain largely unknown.
    Methods: To this end, flow cytometry and scRNAseq were performed on long bone cells from Sost-cre/Ai9
    Results: Clustering analysis isolated osteoblast precursors that expressed
    Conclusion: In sum, distinct populations of osteoblasts/osteocytes were defined at the single cell level. Using this roadmap of gene assembly, we demonstrated unrealized molecular defects across multiple bone cell populations in a mouse model of CKD, and our collective results suggest a potentially earlier and more broad bone pathology in this disease than previously recognized.
    MeSH term(s) Mice ; Animals ; Transcriptome ; Bone and Bones/metabolism ; Osteoblasts/metabolism ; Cortical Bone/metabolism ; Renal Insufficiency, Chronic/pathology ; Membrane Proteins/metabolism ; Sphingomyelin Phosphodiesterase/metabolism
    Chemical Substances Bambi protein, mouse ; Membrane Proteins ; Smpd3 protein, mouse (EC 3.1.4.12) ; Sphingomyelin Phosphodiesterase (EC 3.1.4.12)
    Language English
    Publishing date 2023-01-26
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2592084-4
    ISSN 1664-2392
    ISSN 1664-2392
    DOI 10.3389/fendo.2023.1063083
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Author Correction

    Moetasim Ashfaq / Nathaniel Johnson / Fred Kucharski / Noah S. Diffenbaugh / Muhammad Adnan Abid / Matthew F. Horan / Deepti Singh / Salil Mahajan / Subimal Ghosh / Auroop R. Ganguly / Katherine J. Evans / Shafiqul Islam

    npj Climate and Atmospheric Science, Vol 6, Iss 1, Pp 1-

    The influence of natural variability on extreme monsoons in Pakistan

    2023  Volume 1

    Keywords Environmental sciences ; GE1-350 ; Meteorology. Climatology ; QC851-999
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Phase 2, Double-Blind, Placebo-controlled Trial of a c-Jun N-Terminal Kinase Inhibitor in Idiopathic Pulmonary Fibrosis.

    Mattos, Waldo L L D / Khalil, Nasreen / Spencer, Lisa G / Bonella, Francesco / Folz, Rodney J / Rolf, J Douglass / Mogulkoc, Nesrin / Lancaster, Lisa H / Jenkins, R Gisli / Lynch, David A / Noble, Paul W / Maher, Toby M / Cottin, Vincent / Senger, Stefanie / Horan, Gerald S / Greenberg, Steven / Popmihajlov, Zoran

    American journal of respiratory and critical care medicine

    2024  

    Abstract: ... ...

    Abstract Rationale
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202310-1907OC
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Predicting male dairy calf live weight for use in calf management decision support

    Dunne, F.L. / Kelleher, M.M. / Horan, B. / Evans, R.D. / Berry, D.P.

    JDS communications. 2021 Sept., v. 2, no. 5

    2021  

    Abstract: The growing awareness and scrutiny of the management of young dairy calves, especially male calves, necessitates a support tool to aid in the planning of resource allocation on dairy farms. There is a desire among some vendors for a minimum calf weight ... ...

    Abstract The growing awareness and scrutiny of the management of young dairy calves, especially male calves, necessitates a support tool to aid in the planning of resource allocation on dairy farms. There is a desire among some vendors for a minimum calf weight when purchasing young dairy bull calves. Hence, the objective of the present study was to investigate whether live weight of young calves (approximately 10–50 d old) can be predicted using readily accessible animal-level features, especially features that may be available in advance of birth. A multiple linear regression mixed model was developed with the live weight of 602 dairy bull calves aged between 10 and 42 d as the dependent variable; the age at which an animal is predicted to reach a predefined live weight was then estimated based on the model regression coefficients. Fixed effects included in the multiple regression model were dam parity, gestation length, and parental average genetic merit for relevant traits available in Ireland; namely, birth weight, birth size, and carcass weight. Herd of origin was included as a random effect, with all calves having been sold directly from the farm of birth. Live weight data were recorded at the point of sale when calves were, on average, 26 d old with a mean live weight of 56.6 kg. Animals were randomly assigned to 10 separate (i.e., folds) cross-validation data sets without replacement (i.e., each fold consisted of a different 10% of the data to test the model, with the remaining 90% of data being used to train the model) to quantify the accuracy of prediction. Across all data, the correlation between actual and predicted live weight was 0.76; the regression coefficient of actual live weight on predicted live weight across all data was 0.99. The root mean squared error of prediction varied from 4.40 to 6.66 kg per fold. Across all data, the root mean squared error was 5.61 kg, implying that 68% of live weight predictions were within 5.61 kg of the actual live weight. Given the potential availability of all model features in advance of birth (gestation length can be predicted from ultrasound examination of the pregnant uterus, although substituting parental average genetic merit for gestation length had minimal effect on model performance), predictions can be integrated into a dairy farm decision support tool to aid in the management of labor and infrastructure resources to achieve minimum live weight specifications before sale.
    Keywords birth weight ; carcass weight ; dairy bulls ; dairy calves ; dairy farming ; decision support systems ; farms ; genetic merit ; gestation period ; herds ; infrastructure ; model validation ; prediction ; regression analysis ; resource allocation ; ultrasonics ; uterus ; Ireland
    Language English
    Dates of publication 2021-09
    Size p. 257-261.
    Publishing place Elsevier Inc.
    Document type Article
    ISSN 2666-9102
    DOI 10.3168/jdsc.2021-0078
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Risk factors and survival in patients with COVID-19 in northeastern Brazil.

    Fernandes, Ana Tereza / Rodrigues, Eujessika K / Araújo, Eder R / Formiga, Magno F / Horan, Priscilla K Sá / Ferreira, Ana Beatriz Nunes de Sousa / Barbosa, Humberto A / Barbosa, Paulo S

    PloS one

    2022  Volume 17, Issue 11, Page(s) e0278213

    Abstract: Background: Knowledge about the epidemiology and risk factors surrounding COVID-19 contributes to developing better health strategies to combat the disease.: Objective: This study aimed to establish a survival analysis and identify the risk factors ... ...

    Abstract Background: Knowledge about the epidemiology and risk factors surrounding COVID-19 contributes to developing better health strategies to combat the disease.
    Objective: This study aimed to establish a survival analysis and identify the risk factors for patients with COVID-19 in an upper middle-income city in Brazil.
    Methods: A retrospective cohort study was conducted with 280 hospitalized patients with COVID-19. The eCOVID platform provided data to monitor COVID-19 cases and help the communication between professionals.
    Results: Age ≥ 65 years was associated with decreased survival (54.8%), and females had a lower survival rate than males (p = 0.01). Regarding risk factors, urea concentration (p<0.001), hospital length of stay (p = 0.002), oxygen concentration (p = 0.005), and age (p = 0.02) were associated with death.
    Conclusion: Age, hospital length of stay, high blood urea concentration, and low oxygen concentration were associated with death by COVID-19 in the studied population. These findings corroborate with studies conducted in research centers worldwide.
    MeSH term(s) Female ; Male ; Humans ; Aged ; COVID-19/epidemiology ; Brazil/epidemiology ; Retrospective Studies ; Risk Factors ; Oxygen
    Chemical Substances Oxygen (S88TT14065)
    Language English
    Publishing date 2022-11-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0278213
    Database MEDical Literature Analysis and Retrieval System OnLINE

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