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  • 1
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    Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
    Oxford University Press (OUP) ; 2015
    In:  G3 Genes|Genomes|Genetics Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Details
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Abstract: The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    URL: Article
    DOI: 10.1534/g3.114.015966
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 2629978-1
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  • 2
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    Cost-effectiveness of Aflibercept Monotherapy vs Bevacizumab First Followed by Aflibercept If Needed for Diabetic Macular Edema
    American Medical Association (AMA) ; 2023
    In:  JAMA Ophthalmology Vol. 141, No. 3 ( 2023-03-01), p. 268-
    Details
    In: JAMA Ophthalmology, American Medical Association (AMA), Vol. 141, No. 3 ( 2023-03-01), p. 268-
    Abstract: The DRCR Retina Network Protocol AC showed no significant difference in visual acuity outcomes over 2 years between treatment with aflibercept monotherapy and bevacizumab first with switching to aflibercept for suboptimal response in treating diabetic macular edema (DME). Understanding the estimated cost and cost-effectiveness of these approaches is important. Objective To evaluate the cost and cost-effectiveness of aflibercept monotherapy vs bevacizumab-first strategies for DME treatment. Design, Setting, and Participants This economic evaluation was a preplanned secondary analysis of a US randomized clinical trial of participants aged 18 years or older with center-involved DME and best-corrected visual acuity of 20/50 to 20/320 enrolled from December 15, 2017, through November 25, 2019. Interventions Aflibercept monotherapy or bevacizumab first, switching to aflibercept in eyes with protocol-defined suboptimal response. Main Outcomes and Measures Between February and July 2022, the incremental cost-effectiveness ratio (ICER) in cost per quality-adjusted life-year (QALY) over 2 years was assessed. Efficacy and resource utilization data from the randomized clinical trial were used with health utility mapping from the literature and Medicare unit costs. Results This study included 228 participants (median age, 62 [range, 34-91 years; 116 [51%] female and 112 [49%] male; 44 [19%] Black or African American, 60 [26%] Hispanic or Latino, and 117 [51%] White) with 1 study eye. The aflibercept monotherapy group included 116 participants, and the bevacizumab-first group included 112, of whom 62.5% were eventually switched to aflibercept. Over 2 years, the cost of aflibercept monotherapy was $26 504 (95% CI, $24 796-$28 212) vs $13 929 (95% CI, $11 984-$15 874) for the bevacizumab-first group, a difference of $12 575 (95% CI, $9987-$15 163). The aflibercept monotherapy group gained 0.015 (95% CI, −0.011 to 0.041) QALYs using the better-seeing eye and had an ICER of $837 077 per QALY gained compared with the bevacizumab-first group. Aflibercept could be cost-effective with an ICER of $100 000 per QALY if the price per dose were $305 or less or the price of bevacizumab was $1307 per dose or more. Conclusions and Relevance Variability in individual needs will influence clinician and patient decisions about how to treat specific eyes with DME. While the bevacizumab-first group costs still averaged approximately $14 000 over 2 years, this approach, as used in this study, may confer substantial cost savings on a societal level without sacrificing visual acuity gains over 2 years compared with aflibercept monotherapy.
    Type of Medium: Online Resource
    ISSN: 2168-6165
    URL: Article
    DOI: 10.1001/jamaophthalmol.2022.6142
    Language: English
    Publisher: American Medical Association (AMA)
    Publication Date: 2023
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  • 3
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    Association of Ultra-Widefield Fluorescein Angiography–Identified Retinal Nonperfusion and the Risk of Diabetic Retinopathy Worsening Over Time
    American Medical Association (AMA) ; 2022
    In:  JAMA Ophthalmology Vol. 140, No. 10 ( 2022-10-01), p. 936-
    Details
    In: JAMA Ophthalmology, American Medical Association (AMA), Vol. 140, No. 10 ( 2022-10-01), p. 936-
    Abstract: Presence of predominantly peripheral diabetic retinopathy (DR) lesions on ultra-widefield fluorescein angiography (UWF-FA) was associated with greater risk of DR worsening or treatment over 4 years. Whether baseline retinal nonperfusion assessment is additionally predictive of DR disease worsening is unclear. Objective To assess whether the extent and location of retinal nonperfusion identified on UWF-FA are associated with worsening in Diabetic Retinopathy Severity Scale (DRSS) score or DR treatment over time. Design, Setting, and Participants This cohort study was a prospective, multicenter, longitudinal observational study with data for 508 eyes with nonproliferative DR and gradable nonperfusion on UWF-FA at baseline. All images were graded at a centralized reading center; 200° ultra-widefield (UWF) color images were graded for DR at baseline and annually for 4 years. Baseline 200° UWF-FA images were graded for nonperfused area, nonperfusion index (NPI), and presence of predominantly peripheral lesions on UWF-FA (FA PPL). Interventions Treatment of DR or diabetic macular edema was at investigator discretion. Main Outcomes and Measures Association of baseline UWF-FA nonperfusion extent with disease worsening, defined as either 2 or more steps of DRSS worsening within Early Treatment Diabetic Retinopathy Study fields on UWF-color images or receipt of DR treatment. Results After adjusting for baseline DRSS, the risk of disease worsening over 4 years was higher in eyes with greater overall NPI (hazard ratio [HR] for 0.1-unit increase, 1.11; 95% CI, 1.02-1.21; P  = .02) and NPI within the posterior pole (HR for 0.1-unit increase, 1.35; 95% CI, 1.17-1.56; P   & amp;lt; .001) and midperiphery (HR for 0.1-unit increase, 1.08; 95% CI, 1.00-1.16; P  = .04). In a multivariable analysis adjusting for baseline DRSS score and baseline systemic risk factors, greater NPI (HR, 1.11; 95% CI, 1.02-1.22; P  = .02) and presence of FA PPL (HR, 1.89; 95% CI, 1.35-2.65; P   & amp;lt; .001) remained associated with disease worsening. Conclusions and Relevance This 4-year longitudinal study has demonstrated that both greater baseline retinal nonperfusion and FA PPL on UWF-FA are associated with higher risk of disease worsening, even after adjusting for baseline DRSS score and known systemic risk. These associations between disease worsening and retinal nonperfusion and FA PPL support the increased use of UWF-FA to complement color fundus photography in future efforts for DR prognosis, clinical care, and research.
    Type of Medium: Online Resource
    ISSN: 2168-6165
    URL: Article
    DOI: 10.1001/jamaophthalmol.2022.3130
    Language: English
    Publisher: American Medical Association (AMA)
    Publication Date: 2022
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  • 4
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    Association of Predominantly Peripheral Lesions on Ultra-Widefield Imaging and the Risk of Diabetic Retinopathy Worsening Over Time
    American Medical Association (AMA) ; 2022
    In:  JAMA Ophthalmology Vol. 140, No. 10 ( 2022-10-01), p. 946-
    Details
    In: JAMA Ophthalmology, American Medical Association (AMA), Vol. 140, No. 10 ( 2022-10-01), p. 946-
    Abstract: Ultra-widefield (UWF) imaging improves the ability to identify peripheral diabetic retinopathy (DR) lesions compared with standard imaging. Whether detection of predominantly peripheral lesions (PPLs) better predicts rates of disease worsening over time is unknown. Objective To determine whether PPLs identified on UWF imaging are associated with increased disease worsening beyond the risk associated with baseline Early Treatment Diabetic Retinopathy Study (ETDRS) Diabetic Retinopathy Severity Scale (DRSS) score. Design, Setting, and Participants This cohort study was a prospective, multicenter, longitudinal observational study conducted at 37 US and Canadian sites with 388 participants enrolled between February and December 2015. At baseline and annually through 4 years, 200° UWF-color images were obtained and graded for DRSS at a reading center. Baseline UWF-color and UWF-fluorescein angiography (FA) images were evaluated for the presence of PPL. Data were analyzed from May 2020 to June 2022. Interventions Treatment of DR or diabetic macular edema was at investigator discretion. Main Outcomes and Measures Predominantly peripheral lesions were defined as DR lesions with a greater extent outside vs inside the 7 standard ETDRS fields. Primary outcome was disease worsening defined as worsening 2 steps or more on the DRSS or receipt of DR treatment. Analyses were adjusted for baseline DRSS score and correlation between 2 study eyes of the same participant. Results Data for 544 study eyes with nonproliferative DR (NPDR) were analyzed (182 [50%] female participants; median age, 62 years; 68% White). The 4-year disease worsening rates were 45% for eyes with baseline mild NPDR, 40% for moderate NPDR, 26% for moderately severe NPDR, and 43% for severe NPDR. Disease worsening was not associated with color PPL at baseline (present vs absent: 38% vs 43%; HR, 0.78; 95% CI, 0.57-1.08; P  = .13) but was associated with FA PPL at baseline (present vs absent: 50% vs 31%; HR, 1.72; 95% CI, 1.25-2.36; P   & amp;lt; .001). Conclusions and Relevance Although no association was identified with color PPL, presence of FA PPL was associated with greater risk of disease worsening over 4 years, independent of baseline DRSS score. These results suggest that use of UWF-FA to evaluate retinas peripheral to standard ETDRS fields may improve the ability to predict disease worsening in NPDR eyes. These findings support use of UWF-FA for future DR staging systems and clinical care to more accurately determine prognosis in NPDR eyes.
    Type of Medium: Online Resource
    ISSN: 2168-6165
    URL: Article
    DOI: 10.1001/jamaophthalmol.2022.3131
    Language: English
    Publisher: American Medical Association (AMA)
    Publication Date: 2022
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  • 5
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    Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition
    American Society for Microbiology ; 2023
    In:  mSystems Vol. 8, No. 2 ( 2023-04-27)
    Details
    In: mSystems, American Society for Microbiology, Vol. 8, No. 2 ( 2023-04-27)
    Abstract: Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are “flying blind” with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth ( 〈 32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus -dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners -dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome’s gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/msystems.01003-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2844333-0
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  • 6
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    Sexual behaviour change following HIV testing services: a systematic review and meta‐analysis
    Wiley ; 2020
    In:  Journal of the International AIDS Society Vol. 23, No. 11 ( 2020-11)
    Details
    In: Journal of the International AIDS Society, Wiley, Vol. 23, No. 11 ( 2020-11)
    Abstract: Learning one’s HIV status through HIV testing services (HTS) is an essential step toward accessing treatment and linking to preventive services for those at high HIV risk. HTS may impact subsequent sexual behaviour, but the degree to which this varies by population or is true in the setting of contemporary HIV prevention activities is largely unknown. As part of the 2019 World Health Organization Consolidated Guidelines on HTS, we undertook a systematic review and meta‐analysis to determine the effect of HTS on sexual behaviour. Methods We searched nine electronic databases for studies published between July 2010 and December 2019. We included studies that reported on at least one outcome (condom use [defined as the frequency of condom use or condom‐protected sex], number of sex partners, HIV incidence, STI incidence/prevalence). We included studies that prospectively assessed outcomes and that fit into one of three categories: (1) those evaluating more versus less‐intensive HTS, (2) those of populations receiving HTS versus not and (3) those evaluating outcomes after versus before HTS. We conducted meta‐analyses using random‐effects models. Results and discussion Of 29 980 studies screened, 76 studies were included. Thirty‐eight studies were randomized controlled trials, 36 were cohort studies, one was quasi‐experimental and one was a serial cross‐sectional study. There was no significant difference in condom use among individuals receiving more‐intensive HTS compared to less‐intensive HTS (relative risk [RR]=1.03; 95% CI: 0.99 to 1.07). Condom use was significantly higher after receiving HTS compared to before HTS for individuals newly diagnosed with HIV (RR = 1.65; 95% CI: 1.36 to 1.99) and marginally significantly higher for individuals receiving an HIV‐negative diagnosis (RR = 1.63; 95% CI: 1.01 to 2.62). Individuals receiving more‐intensive HTS reported fewer sex partners at follow‐up than those receiving less‐intensive HTS, but the finding was not statistically significant (mean difference = −0.28; 95% CI: −3.66, 3.10). Conclusions Our findings highlight the importance of using limited resources towards HTS strategies that focus on early HIV diagnosis, treatment and prevention services rather than resources dedicated to supplementing or enhancing HTS with additional counselling or other interventions.
    Type of Medium: Online Resource
    ISSN: 1758-2652 , 1758-2652
    URL: Issue
    URL: Article
    DOI: 10.1002/jia2.v23.11
    DOI: 10.1002/jia2.25635
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2467110-1
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  • 7
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    Cross-talk among myeloid-derived suppressor cells, macrophages, and tumor cells impacts the inflammatory milieu of solid tumors
    Oxford University Press (OUP) ; 2014
    In:  Journal of Leukocyte Biology Vol. 96, No. 6 ( 2014-08-28), p. 1109-1118
    Details
    In: Journal of Leukocyte Biology, Oxford University Press (OUP), Vol. 96, No. 6 ( 2014-08-28), p. 1109-1118
    Abstract: MDSC and macrophages are present in most solid tumors and are important drivers of immune suppression and inflammation. It is established that cross-talk between MDSC and macrophages impacts anti-tumor immunity; however, interactions between tumor cells and MDSC or macrophages are less well studied. To examine potential interactions between these cells, we studied the impact of MDSC, macrophages, and four murine tumor cell lines on each other, both in vitro and in vivo. We focused on IL-6, IL-10, IL-12, TNF-α, and NO, as these molecules are produced by macrophages, MDSC, and many tumor cells; are present in most solid tumors; and regulate inflammation. In vitro studies demonstrated that MDSC-produced IL-10 decreased macrophage IL-6 and TNF-α and increased NO. IL-6 indirectly regulated MDSC IL-10. Tumor cells increased MDSC IL-6 and vice versa. Tumor cells also increased macrophage IL-6 and NO and decreased macrophage TNF-α. Tumor cell-driven macrophage IL-6 was reduced by MDSC, and tumor cells and MDSC enhanced macrophage NO. In vivo analysis of solid tumors identified IL-6 and IL-10 as the dominant cytokines and demonstrated that these molecules were produced predominantly by stromal cells. These results suggest that inflammation within solid tumors is regulated by the ratio of tumor cells to MDSC and macrophages and that interactions of these cells have the potential to alter significantly the inflammatory milieu within the tumor microenvironment.
    Type of Medium: Online Resource
    ISSN: 0741-5400 , 1938-3673
    URL: Article
    DOI: 10.1189/jlb.3A0414-210R
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2014
    detail.hit.zdb_id: 2026833-6
    SSG: 12
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  • 8
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    Development and application of a high throughput one-pot extraction protocol for quantitative LC-MS/MS analysis of phospholipids in serum and lipoprotein fractions in normolipidemic and dyslipidemic subjects
    Elsevier BV ; 2019
    In:  Journal of Chromatography B Vol. 1118-1119 ( 2019-06), p. 137-147
    Details
    In: Journal of Chromatography B, Elsevier BV, Vol. 1118-1119 ( 2019-06), p. 137-147
    Type of Medium: Online Resource
    ISSN: 1570-0232
    URL: Article
    DOI: 10.1016/j.jchromb.2019.04.041
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
    detail.hit.zdb_id: 1491259-4
    SSG: 11
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  • 9
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    Lessons from Suppressive Therapy and Periodic Presumptive Treatment for Bacterial Vaginosis
    Springer Science and Business Media LLC ; 2019
    In:  Current Infectious Disease Reports Vol. 21, No. 10 ( 2019-10)
    Details
    In: Current Infectious Disease Reports, Springer Science and Business Media LLC, Vol. 21, No. 10 ( 2019-10)
    Type of Medium: Online Resource
    ISSN: 1523-3847 , 1534-3146
    URL: Article
    DOI: 10.1007/s11908-019-0688-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2094167-5
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  • 10
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    The vaginal microbiota, high-risk human papillomavirus infection, and cervical cytology: results from a population-based study
    AME Publishing Company ; 2020
    In:  Gynecology and Pelvic Medicine Vol. 3 ( 2020-9), p. 18-18
    Details
    In: Gynecology and Pelvic Medicine, AME Publishing Company, Vol. 3 ( 2020-9), p. 18-18
    Type of Medium: Online Resource
    ISSN: 2617-4499
    URL: Journal
    URL: Article
    DOI: 10.21037/gpm
    DOI: 10.21037/gpm-20-10
    Language: Unknown
    Publisher: AME Publishing Company
    Publication Date: 2020
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