A5091824135- Single-cell and spatial transcriptomics
- HIV Research and Treatment
- Influenza Virus Research Studies
- T-cell and B-cell Immunology
- Hydrology and Sediment Transport Processes
- Fish Ecology and Management Studies
- Cancer-related molecular mechanisms research
- Immune Cell Function and Interaction
- Neuroinflammation and Neurodegeneration Mechanisms
- Freshwater macroinvertebrate diversity and ecology
- Olfactory and Sensory Function Studies
- Extracellular vesicles in disease
- Amphibian and Reptile Biology
- Environmental DNA in Biodiversity Studies
- Fish Biology and Ecology Studies
- Aquatic Invertebrate Ecology and Behavior
- Diabetes and associated disorders
- Functional Brain Connectivity Studies
- Neural dynamics and brain function
- Gene expression and cancer classification
- Insect behavior and control techniques
- Platelet Disorders and Treatments
- Neurogenesis and neuroplasticity mechanisms
- Lepidoptera: Biology and Taxonomy
- Urban Stormwater Management Solutions
Rutgers, The State University of New Jersey
2000-2022
University of California, Berkeley
2016-2020
Alaska Biological Research (United States)
2006
United States Geological Survey
1997
Abstract Cerebrospinal fluid (CSF) protects the central nervous system (CNS) and analyzing CSF aids diagnosis of CNS diseases, but our understanding leukocytes remains superficial. Here, using single cell transcriptomics, we identify a specific location-associated composition transcriptome leukocytes. Multiple sclerosis (MS) – an autoimmune disease increases transcriptional diversity in blood, type including higher abundance cytotoxic phenotype T helper cells. An analytical approach, named...
CD8+ T cell recognition of virus-infected cells is characteristically restricted by major histocompatibility complex (MHC) class I, although rare examples MHC II restriction have been reported in Cd4-deficient mice and a macaque SIV vaccine trial using recombinant cytomegalovirus vector. Here, we demonstrate the presence human leukocyte antigen (HLA) II-restricted responses with antiviral properties small subset HIV-infected individuals. In these individuals, receptor β (TCRβ) analysis...
Sjögren's syndrome (SS) is a complex multisystem autoimmune disease that results in progressive destruction of the exocrine glands. The purpose this study was to characterize epigenetic changes affected gland tissue and describe relationship these known inflammatory processes.A genome-wide DNA methylation performed on human labial salivary (LSG) biopsy samples obtained from 28 female members International Collaborative Clinical Alliance (SICCA) Registry. Gland methylotyped using Illumina...
To determine whether differentially methylated CpGs in synovium-derived fibroblast-like synoviocytes (FLS) of patients with rheumatoid arthritis (RA) were also RA peripheral blood (PB) samples.For this study, 371 genome-wide DNA methylation profiles measured using Illumina HumanMethylation450 BeadChips PB samples from 63 and 31 unaffected control subjects, specifically the cell subsets CD14+ monocytes, CD19+ B cells, CD4+ memory T naive cells.Of 5,532 hypermethylated FLS candidate CpGs,...
Insecticide use in urban areas results the detection of these compounds streams following stormwater runoff at concentrations likely to cause toxicity for stream invertebrates. In this 2013 study, and streambed sediments were analyzed 91 pesticides dissolved water 118 on sediment. Detections included 33 pesticides, including insecticides, fungicides, herbicides, degradates, a synergist. Patterns pesticide occurrence reveal transport sediment-bound pyrethroids, from upland through outfalls...
Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in composition communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral among dendritic cells (DCs) three elite controllers (ECs) HIV-1 infection. To overcome confounding effects donor-to-donor variability, present a generally applicable computational framework for identifying...
We examined relationships between Columbia torrent salamanders (Rhyacotriton kezeri) and biotic abiotic habitat attributes at landscape reach (within-stream) scales in managed forests of northwestern Oregon, USA. In 2000, we found 851 58% 119 headwater (first-order) streams from randomly selected 2.58-km2 sections the study area. Landscape-level variation salamander distribution relative abundance was related to landform features that included parent geology, elevation, aspect, but not age...
Abstract Systematic measurement biases make data normalization an essential preprocessing step in single-cell RNA sequencing (scRNA-seq) analysis. There may be multiple, competing considerations behind the assessment of performance, some them study-specific. Because can have a large impact on downstream results (e.g., clustering and differential expression), it is critically important that practitioners assess performance methods. We developed scone — flexible framework for assessing based...
Although headwater streams constitute a significant portion of stream length within watersheds, their aquatic fauna, contributions to regional biodiversity, and responses forest management have been understudied. Ma cro in ver te brate communities, physical habitat, water chemistry were sampled from 40 managed forests the Oregon Coast Range mountains. We characterized functional structural attributes ma communities relation physical, chemical, biological gradients. Substrate composition,...
Forty-four smallmouth bass Micropterus dolomieu of three size-classes were radio-tracked in Green Lake, Maine, during summer 1993 (10 June–1 September) to determine whether adult size influenced distribution and movement. Large (>406 mm) used deep water (>8 m) more often than did small (248–279 or medium-sized (305–356 the late (15 July–1 September). also found at middepths (4–8 significantly individuals summer. Small fish cover frequently large ones early June–13 July). Both associated with...
To better understand the distribution and abundance of headwater-stream salamanders in managed conifer forests, we examined relationships between Cascade torrent (Rhyacotriton cascadae) biotic abiotic habitat attributes at landscape within-stream levels western Oregon, USA. In 2001 found 145 25% 59 headwater (first-order) streams from randomly selected 2.58-km2 sections study area. Landscape-level variation salamander relative were related to age adjacent riparian forests landform features...
Abstract The upper extent of fish distribution in streams has received increasing attention recent years because fish‐bearing the Pacific Northwest receive greater protection from timber harvest than do non‐fish‐bearing waters. Significant amounts time and funding have been spent surveying for and, more recently, developing models that predict where use ends streams. reliability each approach rests part on assumption can be accurately determined by a single survey boundaries (FDBs) not shift...
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has low-dimensional latent representation. Additional variables account technical effects may erroneously set some observations of to zero. Conditional distributions specified by neural networks, giving proposed enough flexibility fit data well. use variational inference and stochastic optimization approximate posterior distribution. The...
DNA barcoding was applied to select macroinvertebrates from aquatic bioassessment samples collected National Parks and Preserves in Alaska, USA. The finer taxonomic resolution provided by revealed the presence of 28 insect species previously unreported Alaska; 21 these are also new records for USA, 7 North America, excluding Greenland. distributed among Diptera: Ceratopogonidae (1), Chironomidae (20), Limoniidae Tipulidae (1); Ephemeroptera: Baetidae (2); Trichoptera: Apataniidae Goeridae...
Transcranial alternating current stimulation (tACS) is used as a non-invasive tool for cognitive enhancement and clinical applications. The physiological effects of tACS, however, are complex poorly understood (Liu et al. 2018). Most studies tACS focus on its ability to entrain brain oscillations (Herrmann 2013), but our behavioral results in humans (Kar Krekelberg 2014a) extracellular recordings nonhuman primates 2017) support the view that at 10 Hz additionally affects function by reducing...
The larva of the aquatic dance fly genus Proclinopyga Melander is described for first time. larval association with adult stages was facilitated using COI mitochondrial DNA barcode sequences. larvae are found in coarse substrates riffles and other swift-flowing sections streams small rivers. infrequently occur benthic samples collected from these habitat types, where they may co-occur Empididae genera. final instar illustrated a key to genera Clinocerinae North America updated.
Summary Cerebrospinal fluid (CSF) protects the central nervous system (CNS) and analyzing CSF aids diagnosis of CNS diseases, but our understanding leukocytes remains superficial. Here, we firstly provide a transcriptional map single in compared to blood. Leukocyte composition transcriptome were compartment-specific with CSF-enrichment myeloid dendritic cells border-associated phenotype monocytes. We secondly tested how multiple sclerosis (MS) - an autoimmune disease affected both...