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Berlin Brandenburg

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  • MEDLINE/PubMed (NLM)  (74)
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  • 1
    Language: English
    In: Journal of Bacteriology, pp. 6618-6619
    Description: Article discussing the draft genome sequence of the cyanide-utilizing bacterium 'Pseudomonas fluorescens' strain NCIMB 11764.
    Keywords: Pseudomanas Fluorescens ; Genetics ; Cyanide
    ISSN: 00219193
    E-ISSN: 10985530
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  • 2
    Language: English
    In: Plant physiology, May 2012, Vol.159(1), pp.299-310
    Description: Symbiotic nitrogen fixation occurs in nodules, specialized organs on the roots of legumes. Within nodules, host plant cells are infected with rhizobia that are encapsulated by a plant-derived membrane forming a novel organelle, the symbiosome. In Medicago truncatula, the symbiosome consists of the symbiosome membrane, a single rhizobium, and the soluble space between them, called the symbiosome space. The symbiosome space is enriched with plant-derived proteins, including the M. truncatula EARLY NODULIN8 (MtENOD8) protein. Here, we present evidence from green fluorescent protein (GFP) fusion experiments that the MtENOD8 protein contains at least three symbiosome targeting domains, including its N-terminal signal peptide (SP). When ectopically expressed in nonnodulated root tissue, the MtENOD8 SP delivers GFP to the vacuole. During the course of nodulation, there is a nodule-specific redirection of MtENOD8-SP-GFP from the vacuole to punctate intermediates and subsequently to symbiosomes, with redirection of MtENOD8-SP-GFP from the vacuole to punctate intermediates preceding intracellular rhizobial infection. Experiments with M. truncatula mutants having defects in rhizobial infection and symbiosome development demonstrated that the MtNIP/LATD gene is required for redirection of the MtENOD8-SP-GFP from the vacuoles to punctate intermediates in nodules. Our evidence shows that MtENOD8 has evolved redundant targeting sequences for symbiosome targeting and that intracellular localization of ectopically expressed MtENOD8-SP-GFP is useful as a marker for monitoring the extent of development in mutant nodules.
    Keywords: Protein Sorting Signals ; Medicago Truncatula -- Chemistry ; Plant Proteins -- Chemistry ; Vacuoles -- Chemistry
    ISSN: 00320889
    E-ISSN: 1532-2548
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  • 3
    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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  • 4
    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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  • 5
    In: PLoS ONE, 2018, Vol.13(7)
    Description: Objective To predict hospital admission at the time of ED triage using patient history in addition to information collected at triage. Methods This retrospective study included all adult ED visits between March 2014 and July 2017 from one academic and two community emergency rooms that resulted in either admission or discharge. A total of 972 variables were extracted per patient visit. Samples were randomly partitioned into training (80%), validation (10%), and test (10%) sets. We trained a series of nine binary classifiers using logistic regression (LR), gradient boosting (XGBoost), and deep neural networks (DNN) on three dataset types: one using only triage information, one using only patient history, and one using the full set of variables. Next, we tested the potential benefit of additional training samples by training models on increasing fractions of our data. Lastly, variables of importance were identified using information gain as a metric to create a low-dimensional model. Results A total of 560,486 patient visits were included in the study, with an overall admission risk of 29.7%. Models trained on triage information yielded a test AUC of 0.87 for LR (95% CI 0.86–0.87), 0.87 for XGBoost (95% CI 0.87–0.88) and 0.87 for DNN (95% CI 0.87–0.88). Models trained on patient history yielded an AUC of 0.86 for LR (95% CI 0.86–0.87), 0.87 for XGBoost (95% CI 0.87–0.87) and 0.87 for DNN (95% CI 0.87–0.88). Models trained on the full set of variables yielded an AUC of 0.91 for LR (95% CI 0.91–0.91), 0.92 for XGBoost (95% CI 0.92–0.93) and 0.92 for DNN (95% CI 0.92–0.92). All algorithms reached maximum performance at 50% of the training set or less. A low-dimensional XGBoost model built on ESI level, outpatient medication counts, demographics, and hospital usage statistics yielded an AUC of 0.91 (95% CI 0.91–0.91). Conclusion Machine learning can robustly predict hospital admission using triage information and patient history. The addition of historical information improves predictive performance significantly compared to using triage information alone, highlighting the need to incorporate these variables into prediction models.
    Keywords: Research Article ; Medicine And Health Sciences ; Medicine And Health Sciences ; Research And Analysis Methods ; Physical Sciences ; Medicine And Health Sciences ; Computer And Information Sciences ; Biology And Life Sciences ; Physical Sciences ; Research And Analysis Methods ; Medicine And Health Sciences ; Medicine And Health Sciences
    E-ISSN: 1932-6203
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  • 6
    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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  • 7
    Language: English
    In: Oecologia, August 2017, Vol.184(4), pp.859-871
    Description: Elucidating the factors determining reproductive success has challenged scientists since Darwin, but the exact pathways that shape the evolution of life history traits by connecting extrinsic (e.g., landscape structure) and intrinsic (e.g., female's age and endosymbionts) factors and reproductive success have rarely been studied. Here we collected female fleas from wild rodents in plots differing in their densities and proportions of the most dominant rodent species. We then combined path analysis and model selection approaches to explore the network of effects, ranging from micro to macroscales, determining the reproductive success of these fleas. Our results suggest that female reproductive success is directly and positively associated with their infection by Mycoplasma bacteria and their own body mass, and with the rodent species size and total density. In addition, we found evidence for indirect effects of rodent sex and rodent community diversity on female reproductive success. These results highlight the importance of exploring interrelated factors across organization scales while studying the reproductive success of wild organisms, and they have implications for the control of vector-borne diseases.
    Keywords: Fitness ; Life History ; Model Selection ; Parasites ; Path Analysis ; Scales ; Arthropod Vectors ; Flea Infestations ; Reproduction
    ISSN: 00298549
    E-ISSN: 1432-1939
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  • 8
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article discussing a study that was conducted to understand the basis of a bacterial infection that is common among dairy cows.
    Keywords: Dairy ; Cows ; Pyrosequencing ; Amplicons ; Bacteria ; Microbiology
    ISSN: 19326203
    E-ISSN: 19326203
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  • 9
    Language: English
    In: PLoS ONE, 01 January 2014, Vol.9(10), p.e109677
    Description: Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 10
    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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