A5086384009- Reproductive tract infections research
- COVID-19 Clinical Research Studies
- Gut microbiota and health
- Urinary Tract Infections Management
- Respiratory viral infections research
- SARS-CoV-2 and COVID-19 Research
- RNA and protein synthesis mechanisms
- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Reproductive System and Pregnancy
- CRISPR and Genetic Engineering
- Long-Term Effects of COVID-19
- Viral Infections and Vectors
- Syphilis Diagnosis and Treatment
- Adolescent Sexual and Reproductive Health
- Bacterial Infections and Vaccines
- Vector-Borne Animal Diseases
- Urological Disorders and Treatments
- Advanced Drug Delivery Systems
- COVID-19 epidemiological studies
- Plant Virus Research Studies
- Vector-borne infectious diseases
- Innovative Microfluidic and Catalytic Techniques Innovation
- 3D Printing in Biomedical Research
- Plant and Fungal Interactions Research
Chan Zuckerberg Initiative (United States)
2020-2024
Stanford University
2015
Abstract SARS-CoV-2 infection is characterized by peak viral load in the upper airway prior to or at time of symptom onset, an unusual feature that has enabled widespread transmission virus and precipitated a global pandemic. How able achieve high titer absence symptoms remains unclear. Here, we examine host transcriptional response patients with COVID-19 ( n = 93), other 41) non-viral 100) acute respiratory illnesses (ARIs). Compared ARIs, pronounced interferon but attenuated activation...
Abstract The epidemiology of infectious causes meningitis in sub-Saharan Africa is not well understood, and a common cause this region, Mycobacterium tuberculosis (TB), notoriously hard to diagnose. Here we show that integrating cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) with host gene expression-based machine learning classifier (MLC) enhances diagnostic accuracy for TB (TBM) its mimics. 368 HIV-infected Ugandan adults subacute were prospectively enrolled. Total...
Background. Bacterial vaginosis (BV) causes genital inflammation and increases HIV risk, whereas a vaginal microbiota dominated by Lactobacillus species is associated with immune quiescence relative protection. BV treatment reduces inflammation, but it unclear whether this reduction driven decrease in BV-associated bacteria or an increase species.
We studied the host transcriptional response to SARS-CoV-2 by performing metagenomic sequencing of upper airway samples in 238 patients with COVID-19, other viral or non-viral acute respiratory illnesses (ARIs). Compared ARIs, COVID-19 was characterized a diminished innate immune response, reduced expression genes involved toll-like receptor and interleukin signaling, chemokine binding, neutrophil degranulation interactions lymphoid cells. Patients also exhibited significantly proportions...
ABSTRACT Vaginal colonization by fungi may elicit genital inflammation and enhance the risk of adverse reproductive health outcomes, such as HIV acquisition. Cross-sectional studies have linked with an absence bacterial vaginosis (BV), but it is unclear whether shifts in vaginal bacteria alter abundance fungi. swabs collected following topical metronidazole treatment for BV during phase 2b, placebo-controlled trial LACTIN-V, a Lactobacillus crispatus -based live biotherapeutic, were assayed...
Abstract Background Emerging data on the clinical presentation, diagnostics, and outcomes of patients with COVID-19 have largely been presented as case series. Few studies compared these features to other acute respiratory illnesses. Methods We examined all presenting an emergency department in San Francisco, California between February 3 March 31, 2020 illness who were tested for SARS-CoV-2. determined status by PCR metagenomic next generation sequencing (mNGS). demographics, comorbidities,...
Polymeric microspheres represent an injectable platform for controlling the release of a variety biologics; may be combined in modular fashion to achieve temporal two or more biomolecules. Microfluidics offers versatile synthesizing uniform polymeric harboring biologics under relatively mild conditions. Poly(ethylene glycol) (PEG) is bioinert polymer that can easily tailored encapsulate and control biologics. In this study, we report microfluidic synthesis biodegradable PEG-based...
ABSTRACT Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses their roles in public health or tick physiology. To address this, we investigated patterns bacterial viral communities across two field populations western black-legged ticks ( Ixodes pacificus ). Through metatranscriptomic analysis 100 individual ticks, quantified taxon prevalence, abundance,...
Abstract Background Bacterial vaginosis (BV) increases HIV acquisition risk, potentially by eliciting genital inflammation. After BV treatment, the vaginal administration of LACTIN-V, a live biotherapeutic containing Lactobacillus crispatus strain CTV-05, reduced recurrence and inflammation; however, 3 months after product cessation, CTV-05 colonization was only sustained in 48% participants. Results This nested sub-study 32 participants receiving LACTIN-V finds that 72% (23/32) demonstrate...
Abstract Background Bacterial vaginosis (BV) is a proinflammatory genital condition associated with adverse reproductive health outcomes, including increased HIV incidence. However, BV recurrence rates are high after standard antibiotic treatment. While the composition of vaginal microbiota before treatment may be linked to recurrence, it unclear whether preceding immune milieu predictive success. Methods Here we assessed baseline soluble factors or predicted success 1 month metronidazole in...
Author(s): Crawford, Emily D; Acosta, Irene; Ahyong, Vida; Anderson, Erika C; Arevalo, Shaun; Asarnow, Daniel; Axelrod, Shannon; Ayscue, Patrick; Azimi, Camillia S; Azumaya, Caleigh M; Bachl, Stefanie; Bachmutsky, Iris; Bhaduri, Aparna; Brown, Jeremy Bancroft; Batson, Joshua; Behnert, Astrid; Boileau, Ryan Bollam, Saumya R; Bonny, Alain Booth, David; Borja, Michael Jerico B; Buie, Bryan; Burnett, Cassandra E; Byrnes, Lauren Cabral, Katelyn A; Cabrera, Joana P; Caldera, Saharai; Canales,...
Abstract Background Outbreaks of SARS-CoV-2 in long-term care facilities (LTCFs) cause significant morbidity and mortality. Mapping viral transmission within between by combining genomic sequencing with epidemiologic investigations enables targeting infection-control interventions. Methods We conducted weekly surveillance residents staff LTCFs Santa Clara County, California, ≥1 confirmed COVID-19 case March July 2020. Positive samples were referred for whole-genome sequencing....
Abstract Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses their roles in public health or tick physiology. To address this, we investigated patterns bacterial viral communities across two field populations western black-legged ticks ( Ixodes pacificus ). Through metatranscriptomic analysis 100 individual ticks, quantified taxon prevalence, abundance,...
FLASH is a crispr-cas9 technology that enriches for targeted sequences in sequencing libraries. The initial DNA sample undergoes blocking step removes of the 5’ phosphoryl groups fragments, resulting product not amendable downstream adaptor ligation or amplification via standard Illumina-based library preparation. subsequent incorporation CRISPR-cas9 exposes desired regions interest, allowing them to be processed into library. For more information on methods and results, please see paper....
FLASH is a crispr-cas9 technology that enriches for targeted sequences in sequencing libraries. The initial DNA sample undergoes blocking step removes of the 5’ phosphoryl groups fragments, resulting product not amendable downstream adaptor ligation or amplification via standard Illumina-based library preparation. subsequent incorporation CRISPR-cas9 exposes desired regions interest, allowing them to be processed into library. For more information on methods and results, please see paper....
<h3>Background</h3> Bacterial vaginosis (BV) induces genital inflammation and enhances HIV acquisition risk, while vaginal Lactobacillus predominance is associated with mucosal immune quiescence reduced risk. BV treatment reduces proinflammatory cytokines, but it unclear whether this due to reductions in BV-associated anaerobes or an increase spp. We investigated the short-term impact of on milieu microbiome. <h3>Methods</h3> Study participants comprised 48 women BV, all whom were treated...
<h3>Objectives</h3> <i>Tuberculous</i> meningitis(TBM) is a common cause of meningitis in sub-Saharan Africa. CSF PCR with GeneXpert RIF/MTB Ultra only 70% sensitive for detection definite/probable TBM. Many infections can mimic Metagenomic next generation sequencing(mNGS) detect the whole diversity infectious microbes, but be insensitive to TB CSF. We assessed whether leveraging mNGS identify combined machine learning classifier(MLC), based on host transcriptomic data generated by mNGS,...