相关论文: Gut microbiome composition: back to baseline?
Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU…
This work studies fundamental questions regarding the optimal design of antimicrobial treatment protocols, using standard pharmacodynamic and pharmacokinetic mathematical models. We consider the problem of designing an antimicrobial…
Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we…
The large reservoir of antibiotic resistant bacteria in raw and treated water supplies is a matter of public health concern. Currently, the National Antimicrobial Resistance Monitoring Systems, a collaborative effort of the Centers for…
For more than 3.5 billion years, life experienced dramatic environmental extremes on Earth. These include shifts from oxygen-less to over-oxygenated atmospheres and cycling between hothouse conditions and global glaciations. Meanwhile, an…
Bacterial populations often have complex spatial structures, which can impact their evolution. Here, we study how spatial structure affects the evolution of antibiotic resistance in a bacterial population. We consider a minimal model of…
It has long been known that antibiotic treatment will not completely kill off a bacteria population. For many species a small fraction of bacteria is not sensitive to antibiotics. These bacteria are said to persist. Recently it has been…
After birth setting up an effective immune system is a major challenge for all living organisms. In this paper we show that this process can be explored by using the age-specific infant death rate as a kind of sensor. This is made possible…
Bacteria on surfaces exhibit collective behaviors, such as active turbulence and active stresses, which result from their motility, growth, and interactions with their local surroundings. However, interfacial deformations on soft surfaces…
Clinical notes contain information about patients that goes beyond structured data like lab values and medications. However, clinical notes have been underused relative to structured data, because notes are high-dimensional and sparse. This…
Rapid antimicrobial susceptibility testing (AST) is urgently needed for treating infections with correct antibiotics and slowing down the emergence of antibiotic-resistant bacteria. Here, we report a phenotypic platform that rapidly…
Background and Objectives: Proximal catheter obstruction is the leading cause of ventriculoperitoneal shunt failure, yet the biological triggers of peri-catheter inflammation and tissue ingrowth remain poorly defined. Evidence of bacterial…
We studied the swimming of \textit{Escherichia coli} bacteria in the vicinity of the critical point in a solution of the non-ionic surfactant \chem{C_{12}E_{5}} in buffer solution. In phase contrast microscopy, each swimming cell produces a…
High-throughput sequencing technology allows us to test the compositional difference of bacteria in different populations. One important feature of human microbiome data is that it often includes a large number of zeros. Such data can be…
Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…
Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…
The process of infection of a host is complex, influenced by factors such as microbial variation within and between hosts as well as differences in dose across hosts. This study uses dose-response and within-host microbial infection models…
Claims from observational studies often fail to replicate. A study was undertaken to assess the reliability of cohort studies used in a highly cited meta-analysis of the association between ambient nitrogen dioxide, NO2, and fine…
Quantification of microbial interactions from 16S rRNA and meta-genomic sequencing data is difficult due to their sparse nature, as well as the fact that the data only provides measures of relative abundance. In this paper, we propose using…
As antibiotic resistance continues to pose a significant threat to public health, alternative treatments are urgently needed. Phage therapy, which utilizes bacteriophages to specifically target bacterial pathogens, has emerged as a…