The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal ...data. Here, we introduce “weighted-nearest neighbor” analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.
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•“Weighted nearest neighbor” analysis integrates multimodal single-cell data•A multimodal reference “atlas” of the circulating human immune system•Identification and validation of novel sources of lymphoid heterogeneity•“Reference-based” mapping of query datasets onto a multimodal atlas
A framework that allows for the integration of multiple data types using single cells is applied to understand distinct immune cell states, previously unidentified immune populations, and to interpret immune responses to vaccinations.
Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to ...measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to “anchor” diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
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•Seurat v3 identifies correspondences between cells in different experiments•These “anchors” can be used to harmonize datasets into a single reference•Reference labels and data can be projected onto query datasets•Extends beyond RNA-seq to single-cell protein, chromatin, and spatial data
A computational approach to integrate diverse modalities associated with single-cell sequencing datasets can be used to better understand cellular identity and function.
Antibacterial drug discovery and development has slowed considerably in recent years, with novel classes discovered decades ago and regulatory approvals tougher to get. Traditional approaches and the ...newer genomic mining approaches have not yielded novel classes of antibacterial compounds. Instead, improved analogues of existing classes of antibacterial drugs have been developed by improving potency, minimizing resistance and alleviating toxicity.
This article is a comprehensive review of newer classes of antibacterial drugs introduced or approved after year 2000.
It describes their mechanisms of action/resistance, improved analogues, spectrum of activity and clinical trials. It also discusses new compounds in development with novel mechanisms of action, as well as novel unexploited bacterial targets and strategies that may pave the way for combating drug resistance and emerging pathogens in the twenty-first century.
The outlook of antibacterial drug discovery, though challenging, may not be insurmountable in the years ahead, with legislation on incentives and funding introduced for developing an antimicrobial discovery program and efforts to conserve antibacterial drug use.
We present Spitzer Space Telescope variability monitoring observations of three low-gravity L dwarfs with previous detections of variability in the near-IR: 2MASS J0045+16, 2MASS J0501−00, and 2MASS ...J1425−36. We detect significant periodic variability in two of our targets, 2MASS J0045+16 and 2MASS J0501−00. We do not detect variability in 2MASS J1425−36. Combining our new rotation periods with rotational velocities, we calculate inclination angles of 22° 1°, , and for 2MASS J0045+16, 2MASS J0501−00, and 2MASS J1425−36, respectively. Our three new objects are consistent with the tentative relations between inclination, amplitude, and color anomaly previously reported. Objects with the highest variability amplitudes are inclined equator on, while the maximum observed amplitude decreases as the inclination angle decreases. We also find a correlation between the inclination angle and color anomaly for the sample of objects with measured inclinations. Compiling the entire sample of brown dwarfs with Spitzer variability detections, we find no enhancement in amplitude for young, early-L dwarfs compared to the field dwarf population. We find a possible enhancement in amplitude of low-gravity late-L dwarfs at 4.5 m. We do not find a correlation between amplitude ratio and spectral type for field dwarfs or for the young population. Finally, we compile the rotation periods of a large sample of brown dwarfs with ages 1 Myr-1 Gyr and compare the rotation rates predicted by evolutionary models assuming angular momentum conservation. We find that the rotation rates of the current sample of brown dwarfs fall within the expected range set by evolutionary models and breakup limits.
The operating environment of nuclear reactors imposes extreme challenges on the materials from which the structures within and surrounding the reactor are constructed. Understanding the effects of ...exposure to this environment is critical for ensuring the safe long-term operation of these reactors. The Grizzly and BlackBear codes are being developed to model the progression of aging mechanisms and their effects on the integrity of critical structures. These codes take advantage of the capabilities of the MOOSE framework to solve the wide range of coupled physics problems that are encountered in predictive simulation of structural degradation. This paper provides an overview of these codes, with a specific focus on two capabilities relevant for light water reactor applications: reactor pressure vessel embrittlement and concrete degradation.
The continued emergence of Neisseria gonorrhoeae isolates which are resistant to first-line antibiotics has reinvigorated interest in alternative therapies such as expanded use of gentamicin (Gen). ...We hypothesized that expanded use of Gen promotes emergence of gonococci with clinical resistance to this aminoglycoside. To understand how decreased susceptibility of gonococci to Gen might develop, we selected spontaneous low-level Gen-resistant (Gen
) mutants (Gen MIC = 32 μg/mL) of the Gen-susceptible strain FA19. Consequently, we identified a novel missense mutation in
, which encodes elongation factor G (EF-G), causing an alanine (A) to valine (V) substitution at amino acid position 563 in domain IV of EF-G; the mutant allele was termed
. Transformation analysis showed that
could increase the Gen MIC by 4-fold. While possession of
did not impair either
gonococcal growth or protein synthesis, it did result in a fitness defect during experimental infection of the lower genital tract in female mice. Through bioinformatic analysis of whole-genome sequences of 10,634 international gonococcal clinical isolates, other
alleles were frequently detected, but genetic studies revealed that they could not decrease Gen susceptibility in a similar manner to
. In contrast to these diverse international
alleles, the
encoded A563V substitution was detected in only a single gonococcal clinical isolate. We hypothesize that the rare occurrence of
in N. gonorrhoeae clinical isolates is likely due to a fitness cost during infection, but compensatory mutations which alleviate this fitness cost could emerge and promote Gen
in global strains.
The acoustic fluid‐structure interaction (FSI) formulation is a practical numerical approach for the seismic analysis of fluid‐filled tanks. However, there are no verification and validation studies ...reported in the literature that demonstrate the ability of an acoustic FSI numerical model to predict responses important to structural and mechanical design for intense translational and rotational earthquake inputs. Herein, an acoustic FSI formulation is implemented in the open‐source Multiphysics Object‐Oriented Simulation Environment (MOOSE), and is formally verified and validated using analytical solutions and code‐to‐code verification, and experimental data, respectively. The analytical solutions are for small amplitude, unidirectional seismic inputs. The code‐to‐code verification utilizes a previously verified and validated Arbitrary Lagrangian‐Eulerian (ALE) numerical model in the commercial finite element code LS‐DYNA. The validation studies utilize a comprehensive data set assembled from results of 3D earthquake‐simulator tests of a fluid‐filled vessel. The acoustic numerical model in MOOSE is verified and validated for hydrodynamic pressures and support reactions except for cases that involve significant convective response. For small amplitude inputs, numerically predicted wave heights match those of the analytical solutions. The numerical model is not verified and validated for wave height calculations under intense 3D seismic inputs. The run times for the acoustic FSI simulations in MOOSE are an order of magnitude, or more, shorter than for the corresponding ALE simulations in LS‐DYNA. The utility of the MOOSE acoustic FSI implementation is demonstrated by seismic analysis of a building equipped with a fluid‐filled, advanced nuclear reactor.
In the past decade, minimally invasive approaches have been developed for aortic valve surgery. We reviewed our data to determine if the use of the PORT ACCESS technique has improved hospital ...morbidity and mortality.
Data were collected on 90 patients who had a replacement of their aortic valve using PORT ACCESS procedures (PORT ACCESS aortic valve replacement PAVR). This group was then matched 1:4 to a control group having aortic valve replacement surgery using a standard sternotomy approach.
The two groups had no statistically significant differences in preoperative risk factors. The perioperative and 30-day outcomes from the matched AVR and PAVR groups showed no mortalities in the PAVR group and 3.1% in the AVR group. Mean length of stay was shorter for PAVR patients (7.2 +/- 5.0 days; median 6 days) compared with the mean stay in the sternotomy group (8.5 +/- 9.5 days; median 6 days), PAVR patients also had statistically significant shorter intensive care unit stays, and time on ventilator. The number of patients needing ventilator support postoperatively was significantly lower in the PORT ACCESS group. Cross-clamp and perfusion times were longer in the PAVR group. No other morbidity was significantly different between groups, except for postoperative tamponade (higher in PAVR group).
In this analysis of matched patients, the patients having aortic valve replacement using PORT ACCESS procedures, spent a shorter time in the intensive care unit and had less need for postoperative ventilator usage (both number of patients using a ventilator and the mean time of use) in comparison with patients undergoing conventional sternotomy.
It is known that ethacrynic acid (EA) decreases the intracellular levels of glutathione. Whether the anticipated oxidative stress affects the structural integrity of DNA is unknown. Therefore, DNA ...damage was assessed in EA-treated HCT116 cells, and the impact of several antioxidants was also determined. EA caused both concentration-dependent and time-dependent DNA damage that eventually resulted in cell death. Unexpectedly, the DNA damage caused by EA was intensified by either ascorbic acid or trolox. In contrast, EA-induced DNA damage was reduced by N-acetylcysteine and by the iron chelator, deferoxamine. In elucidating the DNA damage, it was determined that EA increased the production of reactive oxygen species, which was inhibited by N-acetylcysteine and deferoxamine but not by ascorbic acid and trolox. Also, EA decreased glutathione levels, which were inhibited by N-acetylcysteine. But, ascorbic acid, trolox, and deferoxamine neither inhibited nor enhanced the capacity of EA to decrease glutathione. Interestingly, the glutathione synthesis inhibitor, buthionine sulfoxime, lowered glutathione to a similar degree as EA, but no noticeable DNA damage was found. Nevertheless, buthionine sulfoxime potentiated the glutathione-lowering effect of EA and intensified the DNA damage caused by EA. Additionally, in examining redox-sensitive stress gene expression, it was found that EA increased HO-1, GADD153, and p21mRNA expression, in association with increased nuclear localization of Nrf-2 and p53 proteins. In contrast to ascorbic acid, trolox, and deferoxamine, N-acetylcysteine suppressed the EA-induced upregulation of GADD153, although not of HO-1. Overall, it is concluded that EA has genotoxic properties that can be amplified by certain antioxidants.
•Ethacrynic acid (EA) caused cellular DNA damage.•EA-induced DNA damage was potentiated by ascorbic acid or trolox.•EA increased ROS production, not inhibited by ascorbic acid or trolox.•EA decreased glutathione levels, not prevented by ascorbic acid or trolox.•Buthionine sulfoxime intensified the DNA damage caused by EA.
Refugee resettlement is a complex process relevant to migration medicine. A partnership between the International Organization for Migration, the US Centers for Disease Control and Prevention, and ...the University of Minnesota addresses medical needs of refugees and serves as a model for improving the continuum of care delivered to refugees.
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