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  • 1
    Language: English
    In: PLoS One, CA: Public Library of Science
    Description: This article explores the interrelationship between the urinary microbiota and host antimicrobial peptides as mechanisms for urinary tract infection risk.
    Keywords: Resident Bacterial Communities ; Host Antimicrobial Peptides ; Urinary Tract Infection
    ISSN: 19326203
    E-ISSN: 19326203
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  • 2
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article discussing the microbial communities in male first catch urine and how these are highly similar to those paired in urethral swab specimens.
    Keywords: Microbials ; Bacteria ; Urine
    ISSN: 19326203
    E-ISSN: 19326203
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  • 3
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article discussing the bacterial composition of subgingival plaque among diabetic and non-diabetic subjects to determine the effect that diabetes mellitus has on dental health.
    Keywords: Periodontiitis ; Bacteria ; Diabetes ; Pyrosequencing
    ISSN: 19326203
    E-ISSN: 19326203
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  • 4
    In: PLoS ONE, 2017, Vol.12(8)
    Description: Several ecological hypotheses ( e . g ., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell’s neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al .’s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports ). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher’s exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity ( i . e ., the exhibition or ‘phenotype’ of community assembly), it does not seem to cause the ‘mutation’ of the ‘genotype” (mechanism) of community assembly. We argue that the ‘phenotypic’ changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.
    Keywords: Research Article ; Medicine And Health Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences ; Biology And Life Sciences ; Ecology And Environmental Sciences
    E-ISSN: 1932-6203
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  • 5
    In: PLoS ONE, 2018, Vol.13(3)
    Description: Background Urinary tract infection (UTI) is a common emergency department (ED) diagnosis with reported high diagnostic error rates. Because a urine culture, part of the gold standard for diagnosis of UTI, is usually not available for 24–48 hours after an ED visit, diagnosis and treatment decisions are based on symptoms, physical findings, and other laboratory results, potentially leading to overutilization, antibiotic resistance, and delayed treatment. Previous research has demonstrated inadequate diagnostic performance for both individual laboratory tests and prediction tools. Objective Our aim, was to train, validate, and compare machine-learning based predictive models for UTI in a large diverse set of ED patients. Methods Single-center, multi-site, retrospective cohort analysis of 80,387 adult ED visits with urine culture results and UTI symptoms. We developed models for UTI prediction with six machine learning algorithms using demographic information, vitals, laboratory results, medications, past medical history, chief complaint, and structured historical and physical exam findings. Models were developed with both the full set of 211 variables and a reduced set of 10 variables. UTI predictions were compared between models and to proxies of provider judgment (documentation of UTI diagnosis and antibiotic administration). Results The machine learning models had an area under the curve ranging from 0.826–0.904, with extreme gradient boosting (XGBoost) the top performing algorithm for both full and reduced models. The XGBoost full and reduced models demonstrated greatly improved specificity when compared to the provider judgment proxy of UTI diagnosis OR antibiotic administration with specificity differences of 33.3 (31.3–34.3) and 29.6 (28.5–30.6), while also demonstrating superior sensitivity when compared to documentation of UTI diagnosis with sensitivity differences of 38.7 (38.1–39.4) and 33.2 (32.5–33.9). In the admission and discharge cohorts using the full XGboost model, approximately 1 in 4 patients (4109/15855) would be re-categorized from a false positive to a true negative and approximately 1 in 11 patients (1372/15855) would be re-categorized from a false negative to a true positive. Conclusion The best performing machine learning algorithm, XGBoost, accurately diagnosed positive urine culture results, and outperformed previously developed models in the literature and several proxies for provider judgment. Future prospective validation is warranted.
    Keywords: Research Article ; Medicine And Health Sciences ; Medicine And Health Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Medicine And Health Sciences ; Biology And Life Sciences ; Medicine And Health Sciences ; Medicine And Health Sciences ; Research And Analysis Methods ; Physical Sciences ; Medicine And Health Sciences ; Physical Sciences ; Research And Analysis Methods ; Computer And Information Sciences ; Computer And Information Sciences
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: PLoS ONE, 2012, Vol.7(5), p.e36298
    Description: Lactobacillus- dominated vaginal microbiotas are associated with reproductive health and STI resistance in women, whereas altered microbiotas are associated with bacterial vaginosis (BV), STI risk and poor reproductive outcomes. Putative vaginal taxa have been observed in male first-catch urine, urethral swab and coronal sulcus (CS) specimens but the significance of these observations is unclear. We used 16 S rRNA sequencing to characterize the microbiota of the CS and urine collected from 18 adolescent men over three consecutive months. CS microbiotas of most participants were more stable than their urine microbiotas and the composition of CS microbiotas were strongly influenced by circumcision. BV-associated taxa, including Atopobium , Megasphaera , Mobiluncus , Prevotella and Gemella , were detected in CS specimens from sexually experienced and inexperienced participants. In contrast, urine primarily contained taxa that were not abundant in CS specimens. Lactobacilllus and Streptococcus were major urine taxa but their abundance was inversely correlated. In contrast, Sneathia , Mycoplasma and Ureaplasma were only found in urine from sexually active participants. Thus, the CS and urine support stable and distinct bacterial communities. Finally, our results suggest that the penis and the urethra can be colonized by a variety of BV-associated taxa and that some of these colonizations result from partnered sexual activity.
    Keywords: Research Article ; Biology ; Medicine ; Public Health And Epidemiology ; Infectious Diseases ; Microbiology ; Urology
    E-ISSN: 1932-6203
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  • 7
    Language: English
    In: The Journal of biological chemistry, 20 April 2018, Vol.293(16), pp.6064-6074
    Description: Adiponectin is an adipocyte-derived hormone with antidiabetic activities that include increasing the sensitivity of cells to insulin. Adaptor protein containing pleckstrin homology domain, phosphotyrosine-binding domain, and leucine zipper motif (APPL1) stimulates adiponectin signaling and promotes adiponectin's insulin-sensitizing effects by binding to two adiponectin receptors, AdipoR1 and AdipoR2, and the insulin receptor. In this study, we report an alternative splicing variant of APPL1 (APPL1sv) that is highly expressed in mouse liver, pancreas, and spleen tissues. The expression levels of APPL1sv in liver tissues were enhanced in a mouse model of obesity and diabetic dyslipidemia ( db/db mice) and reduced in calorie-restricted mice compared with -fed mice. APPL1sv overexpression or suppression inhibited or enhanced, respectively, adiponectin-stimulated phosphorylation of AMP protein kinase (AMPK) in mouse hepatocytes. We also found that APPL1sv binds to AdipoR1 and AdipoR2 under basal conditions and that adiponectin treatment reduces this binding. Overexpression of APPL1sv blocked adiponectin-induced interactions of APPL1 with the adiponectin receptors. Moreover, adenovirus-mediated and short hairpin RNA-based suppression of APPL1sv greatly reduced high fat diet-induced insulin resistance and hepatic glucose production in mice. Our study identifies a key suppressor of hepatic adiponectin signaling and insulin sensitivity, a finding that may shed light on identifying effective therapeutic targets for treating insulin resistance and type 2 diabetes.
    Keywords: Amp-Activated Kinase (Ampk) ; Appl1 ; Appl1sv ; Adiponectin ; Alternative Splicing ; Diabetes ; Insulin Resistance ; Liver ; Metabolic Disorder ; Metabolism ; Alternative Splicing ; Insulin Resistance ; Signal Transduction ; Adaptor Proteins, Signal Transducing -- Genetics ; Adiponectin -- Metabolism ; Liver -- Metabolism ; Obesity -- Genetics
    E-ISSN: 1083-351X
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  • 8
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article discussing research on characteristic male urine microbiomes associated with asymptomatic sexually transmitted infection.
    Keywords: Microbiomes ; Infections ; Bacteria ; Urine
    ISSN: 19326203
    E-ISSN: 19326203
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  • 9
    In: Critical Care Medicine, 2017, Vol.45(6), pp.e543-e551
    Description: OBJECTIVES:: Characterization of urinary bacterial microbiome and antimicrobial peptides after burn injury to identify potential mechanisms leading to urinary tract infections and associated morbidities in burn patients. DESIGN:: Retrospective cohort study using human urine from control and burn subjects. SETTING:: University research laboratory. PATIENTS:: Burn patients. INTERVENTIONS:: None. MEASUREMENTS AND MAIN RESULTS:: Urine samples from catheterized burn patients were collected hourly for up to 40 hours. Control urine was collected from “healthy” volunteers. The urinary bacterial microbiome and antimicrobial peptide levels and activity were compared with patient outcomes. We observed a significant increase in urinary microbial diversity in burn patients versus controls, which positively correlated with a larger percent burn and with the development of urinary tract infection and sepsis postadmission, regardless of age or gender. Urinary psoriasin and β-defensin antimicrobial peptide levels were significantly reduced in burn patients at 1 and 40 hours postadmission. We observed a shift in antimicrobial peptide hydrophobicity and activity between control and burn patients when urinary fractions were tested against Escherichia coli and Enterococcus faecalis urinary tract infection isolates. Furthermore, the antimicrobial peptide activity in burn patients was more effective against E. coli than E. faecalis. Urinary tract infection–positive burn patients with altered urinary antimicrobial peptide activity developed either an E. faecalis or Pseudomonas aeruginosa urinary tract infection, suggesting a role for urinary antimicrobial peptides in susceptibility to select uropathogens. CONCLUSIONS:: Our data reveal potential links for urinary tract infection development and several morbidities in burn patients through alterations in the urinary microbiome and antimicrobial peptides. Overall, this study supports the concept that early assessment of urinary antimicrobial peptide responses and the bacterial microbiome may be used to predict susceptibility to urinary tract infections and sepsis in burn patients.
    Keywords: Medicine;
    ISSN: 0090-3493
    E-ISSN: 15300293
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  • 10
    Language: English
    In: Journal of Clinical Microbiology, pp. 1376-1383
    Description: Article on evidence of uncultivated bacteria in the adult female bladder.
    Keywords: Uropathogens ; Clinical Cultivation ; Uncultivated Bacteria ; Urinary Tract Conditions
    ISSN: 1098660X
    E-ISSN: 1098660X
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