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  • 1
    In: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, Elsevier BV, ( 2024-4)
    Type of Medium: Online Resource
    ISSN: 2451-9022
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2024
    detail.hit.zdb_id: 2879089-3
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  • 2
    In: Nature, Springer Science and Business Media LLC, Vol. 474, No. 7353 ( 2011-6), p. 616-619
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    RVK:
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
    SSG: 11
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  • 3
    In: Scientific Data, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2023-08-21)
    Abstract: During the past decade, cognitive neuroscience has been calling for population diversity to address the challenge of validity and generalizability, ushering in a new era of population neuroscience. The developing Chinese Color Nest Project (devCCNP, 2013–2022), the first ten-year stage of the lifespan CCNP (2013–2032), is a two-stages project focusing on brain-mind development. The project aims to create and share a large-scale, longitudinal and multimodal dataset of typically developing children and adolescents (ages 6.0–17.9 at enrolment) in the Chinese population. The devCCNP houses not only phenotypes measured by demographic, biophysical, psychological and behavioural, cognitive, affective, and ocular-tracking assessments but also neurotypes measured with magnetic resonance imaging (MRI) of brain morphometry, resting-state function, naturalistic viewing function and diffusion structure. This Data Descriptor introduces the first data release of devCCNP including a total of 864 visits from 479 participants. Herein, we provided details of the experimental design, sampling strategies, and technical validation of the devCCNP resource. We demonstrate and discuss the potential of a multicohort longitudinal design to depict normative brain growth curves from the perspective of developmental population neuroscience. The devCCNP resource is shared as part of the “Chinese Data-sharing Warehouse for In-vivo Imaging Brain” in the Chinese Color Nest Project (CCNP) – Lifespan Brain-Mind Development Data Community ( https://ccnp.scidb.cn ) at the Science Data Bank.
    Type of Medium: Online Resource
    ISSN: 2052-4463
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2775191-0
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  • 4
    In: The Journal of Infectious Diseases, Oxford University Press (OUP), Vol. 227, No. 7 ( 2023-04-12), p. 917-925
    Abstract: Neisseria gonorrhoeae is a major public health problem due to increasing incidence and antimicrobial resistance. Genetic markers of reduced susceptibility have been identified; the extent to which those are representative of global antimicrobial resistance is unknown. We evaluated the performance of whole-genome sequencing (WGS) used to predict susceptibility to ciprofloxacin and other antimicrobials using a global collection of N. gonorrhoeae isolates. Methods Susceptibility testing of common antimicrobials and the recently developed zolifodacin was performed using agar dilution to determine minimum inhibitory concentrations (MICs). We identified resistance alleles at loci known to contribute to antimicrobial resistance in N. gonorrhoeae from WGS data. We tested the ability of each locus to predict antimicrobial susceptibility. Results A total of 481 N. gonorrhoeae isolates, collected between 2004 and 2019 and making up 457 unique genomes, were sourced from 5 countries. All isolates with demonstrated susceptibility to ciprofloxacin (MIC ≤0.06 μg/mL) had a wild-type gyrA codon 91. Multilocus approaches were needed to predict susceptibility to other antimicrobials. All isolates were susceptible to zoliflodacin, defined by an MIC ≤0.25 μg/mL. Conclusions Single marker prediction can be used to inform ciprofloxacin treatment of N. gonorrhoeae infection. A combination of molecular markers may be needed to determine susceptibility for other antimicrobials.
    Type of Medium: Online Resource
    ISSN: 0022-1899 , 1537-6613
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1473843-0
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  • 5
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 73, No. 9 ( 2021-11-02), p. e2970-e2975
    Abstract: To highlight geographic differences and the socio-structural determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) test positivity within Los Angeles County (LAC). Methods A geographic information system was used to integrate, map, and analyze SARS-CoV-2 testing data reported by the LAC Department of Public Health and data from the American Community Survey. Structural determinants included race/ethnicity, poverty, insurance status, education, and population and household density. We examined which factors were associated with positivity rates, using a 5% test positivity threshold, with spatial analysis and spatial regression. Results Between 1 March and 30 June 2020 there were 843 440 SARS-CoV-2 tests and 86 383 diagnoses reported, for an overall positivity rate of 10.2% within the study area. Communities with high proportions of Latino/a residents, those living below the federal poverty line, and with high household densities had higher crude positivity rates. Age- adjusted diagnosis rates were significantly associated with the proportion of Latino/as, individuals living below the poverty line, and population and household density. Conclusions There are significant local variations in test positivity within LAC and several socio-structural determinants contribute to ongoing disparities. Public health interventions, beyond shelter in place, are needed to address and target such disparities.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2002229-3
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  • 6
    In: PLOS ONE, Public Library of Science (PLoS), Vol. 16, No. 9 ( 2021-9-27), p. e0255878-
    Abstract: The COVID-19 pandemic illuminated the benefits of telemedicine. Self-collected specimens are a promising alternative to clinician-collected specimens when in-person testing is not feasible. In this study, we assessed the adequacy of self-collected pharyngeal and rectal specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae among individuals undergoing chlamydia and gonorrhea screening. Methods We used data from a large cohort study that included male and female adolescents between the ages of 12–24 years. We considered self-collected specimens adequate for clinical use if the human synthase gene (a control target of the assay) was detected in the specimen. Results In total, 2,458 specimens were included in the analysis. The human synthase gene was detected in 99.2% (2,439/2,458) of all self-collected specimens, 99.5% (1,108/1,114) of the pharyngeal specimens, and 99.0% (1,331/1,344) of the rectal specimens. Conclusion Self-collected pharyngeal and rectal specimens demonstrated a very high proportion of human gene presence, suggesting that self-collection was accurate. A limitation of this study is that the sample adequacy control detects the presence or absence of the human hydroxymethylbilane synthase gene, but it does not indicate the specific anatomic origin of the human hydroxymethylbilane synthase gene. Self-collected specimens may be an appropriate alternative to clinician-collected specimens.
    Type of Medium: Online Resource
    ISSN: 1932-6203
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2021
    detail.hit.zdb_id: 2267670-3
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  • 7
    Online Resource
    Online Resource
    American Society for Microbiology ; 2022
    In:  Microbiology Spectrum Vol. 10, No. 2 ( 2022-04-27)
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 10, No. 2 ( 2022-04-27)
    Abstract: Antimicrobial resistance in N. gonorrhoeae is increasing globally, and ceftriaxone is the recommended treatment for empirical therapy in most settings. Developing molecular assays to detect decreased ceftriaxone susceptibility is critical. Using PathogenWatch, a public database of N. gonorrhoeae genomes, antibiotic susceptibility data and DNA sequences of different genes associated with ceftriaxone resistance were extracted. That information was used to determine the sensitivity and specificity of different molecular markers and algorithms to predict decreased susceptibility to ceftriaxone. A total of 12,943 N. gonorrhoeae genomes were extracted from the PathogenWatch database, of which 9,540 genomes were used in the analysis. The sensitivity and specificity of specific molecular markers and algorithms were largely consistent with prior reports. Small variation ( 〈 10%) in either sensitivity or specificity occurred. Certain algorithms using different molecular markers at various prevalence of decreased ceftriaxone susceptibility identified a potentially clinically useful range of positive and negative predictive values. We validated previously described mutations and algorithms in a large public database containing a global collection of N. gonorrhoeae genomes. Certain mutations and algorithms resulted in sensitivity and specificity values consistent with those of prior studies. Further research is needed to integrate these markers and algorithms into the development of molecular assays to predict decreased ceftriaxone susceptibility. IMPORTANCE Antimicrobial resistance in Neisseria gonorrhoeae ( N. gonorrhoeae ), the causative agent of gonorrhea, is rising globally. Ceftriaxone is the last remaining antibiotic for empirical treatment of gonorrhea. Developing molecular tests to predict ceftriaxone resistance can help to improve detection and surveillance of ceftriaxone resistance. Here, we utilized PathogenWatch, a public global online database of N. gonorrhoeae genomes, to evaluate different genetic markers in predicting decreased susceptibility to ceftriaxone. We compiled MICs for ceftriaxone from the PathogenWatch database and used a computational approach to extract all the genetic markers from the genomic data. We determined the sensitivity and specificity for predicting decreased ceftriaxone susceptibility among several combinations of genetic markers. We identified several combinations of genetic markers with high predictive values for decreased susceptibility to ceftriaxone. These combinations of genetic markers might be promising candidates for future molecular tests to predict ceftriaxone resistance.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 2807133-5
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  • 8
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2022
    In:  Open Forum Infectious Diseases Vol. 9, No. Supplement_2 ( 2022-12-15)
    In: Open Forum Infectious Diseases, Oxford University Press (OUP), Vol. 9, No. Supplement_2 ( 2022-12-15)
    Abstract: Nontyphoidal salmonellosis (NTS) is the second-most common foodborne illness in the US, but extraintestinal manifestations are rare. We describe a case of sternocleidomastoid (SCM) pyomyositis, a rare entity, caused by Salmonella enterica, further delineated by whole-genome sequencing (WGS). A 55 year old male with liver cirrhosis and uncontrolled type-II diabetes mellitus presented with a six-day history of an enlarging left-sided neck mass. He had no fevers, chills, night sweats, nausea, vomiting or diarrhea. He had recently returned from Saudia Arabia with exposures to camels, bats and lemurs. He did not consume raw foods or dairy products. Physical exam revealed normal vital signs and a large firm neck mass. Labs were notable for leukocytosis and hyperglycemia. Neck computed tomography revealed a 6 cm heterogeneous mass inseparable from the left SCM. He required repeated drainage procedures; histopathology revealed skeletal muscle with inflammation, but no malignancy. Blood and procedural cultures grew Salmonella group B. He was treated with ceftriaxone then trimethoprim-sulfamethoxazole. Follow-up 4 weeks after presentation revealed only residual induration. Methods WGS was performed using Illumina MiSeq. Genotype and antimicrobial resistance markers were identified using MLST, KmerFinder and ResFinder on Center of Genomic Epidemiology. Virulence factors were identified using VFanalyzer. Results The bacteria was identified as Salmonella enterica subspecies enterica serovar Typhimurium and typed as ST19, the major phylogroup of Typhimurium globally. Characteristics associated with invasive NTS (iNTS) identified by WGS included genes encoding Type III secretion system and Invasin A. Other virulence factors included fimbrial adherence determinants, macrophage inducible genes, and an intracellular toxin SpvB. Resistance genes included aac(6')-Iaa, which confers resistance to tobramycin and amikacin, and qnrB19, which predicts resistance to ciprofloxacin. However, no quinolone resistance-related mutations were detected in gyrA, gyrB, parC and parE genes. AMR Genes Antimicrobial resistance genes identified by whole-genome sequencing of the Salmonella isolate. Conclusion Patients with uncontrolled diabetes are at increased risk of iNTS with or without associated diarrhea. WGS can identify additional factors that may influence morbidity and resistance. Disclosures All Authors: No reported disclosures.
    Type of Medium: Online Resource
    ISSN: 2328-8957
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2757767-3
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  • 9
    In: Open Forum Infectious Diseases, Oxford University Press (OUP), Vol. 9, No. Supplement_2 ( 2022-12-15)
    Abstract: Pre-exposure prophylaxis (PrEP) is highly effective for HIV prevention and is being scaled up globally. Patients on PrEP have high rates of bacterial STIs, like Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), thus routine screening is recommended. However, access to screening tests for STIs are limited in many low-resource settings. The objectives of this study were to determine the prevalence of CT and NG among participants in Vietnam’s first PrEP program. Methods From January through April 2022 participants in the PrEP program at the Sexual Health Promotion Clinic in Hanoi, Vietnam were recruited to study STI prevalence. Study participants completed a survey collecting demographic, behavioral and clinical characteristics. Participants self-collected urine, rectal, and pharyngeal specimens for nucleic-acid testing. Participants positive for NG had an additional specimen collected for culture and antibiotic susceptibility. Results In total, 108 participants were enrolled, median age was 24 years (IQR: 22– 28). All were male and reported having sex with men in the prior 12 months. The median number of sex partners in the prior 1 month was 1 (IQR: 1 – 2). Symptoms within the prior week were reported by 41.7% (45/108) – 19.4% reported rectal, 15.7% reported urethral, and 26.9% reported pharyngeal symptoms. The overall prevalence of CT or NG infections was 31.5% (34/108). The prevalence of CT was 24.1% (26/108); by anatomic site, there were 17 (15.7%) rectal, 10 (9.3%) pharyngeal, and 6 (5.6%) urethral infections. The prevalence of NG was 13.0% (14/108); there were 12 (11.1%) pharyngeal, 9 (8.3%) rectal, and 0 urethral infections. Among participants reporting any symptoms, CT prevalence was 26.7% (12/45) and NG prevalence 13.3% (6/45). All infections were treated. Conclusion The prevalence of CT and NG was very high among this population of young MSM in a PrEP program in Hanoi, Vietnam. A high proportion of CT infections were rectal (65%) and 86% of NG infections were pharyngeal. These findings highlight the need for expanded access to extragenital nucleic-acid testing among PrEP programs in low- and middle-income countries. Studies demonstrating the benefit of CT/NG screening and treatment within PrEP programs are urgently needed. Disclosures Jeffrey Klausner, MD MPH, Cepheid: Advisor/Consultant|Cepheid: Grant/Research Support|Cepheid: Research equipment and supplies.
    Type of Medium: Online Resource
    ISSN: 2328-8957
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2757767-3
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  • 10
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Journal of Antimicrobial Chemotherapy Vol. 76, No. 11 ( 2021-10-11), p. 2847-2849
    In: Journal of Antimicrobial Chemotherapy, Oxford University Press (OUP), Vol. 76, No. 11 ( 2021-10-11), p. 2847-2849
    Abstract: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is an urgent global health threat. Zoliflodacin is a novel antibiotic undergoing clinical trials for the treatment of gonorrhoea. While there are limited data regarding zoliflodacin resistance in N. gonorrhoeae, three amino acid mutations have been associated with increased MICs of zoliflodacin. Objectives To determine the prevalence of three amino acid mutations associated with zoliflodacin resistance within a large, public database of nearly 13 000 N. gonorrhoeae genomes. Methods PathogenWatch is an online genomic epidemiology platform with a public database of N. gonorrhoeae genomes. That database was used to extract gyrB sequence data and a Basic Local Alignment Search Tool (BLAST) search was performed to identify any of the three amino acid mutations in GyrB that are associated with increased zoliflodacin MICs: D429N, K450N or K450T. As a control for the search methodology, all GyrA sequences were also extracted and S91F mutations were identified and compared with the PathogenWatch database. Results In total, 12 493 N. gonorrhoeae genomes from the PathogenWatch database were included. Among those genomes, none was identified that harboured any of the three mutations associated with increased zoliflodacin MICs. One genome was identified to have a mutation at position 429 in GyrB (D429V). Conclusions The findings suggest that the prevalence of the three mutations associated with zoliflodacin resistance in N. gonorrhoeae is very low. However, further research into the mechanisms of zoliflodacin resistance in N. gonorrhoeae is needed. Genomic epidemiology platforms like PathogenWatch can be used to enhance the global surveillance of AMR.
    Type of Medium: Online Resource
    ISSN: 0305-7453 , 1460-2091
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1467478-6
    SSG: 15,3
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