The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the ...accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.
Early identification and intervention for developmental disorders are critical to the well-being of children and are the responsibility of pediatric professionals as an integral function of the ...medical home. This report models a universal system of developmental surveillance and screening for the early identification of conditions that affect children's early and long-term development and achievement, followed by ongoing care. These conditions include autism, deafness/hard-of-hearing, intellectual and motor disabilities, behavioral conditions, and those seen in other medical conditions. Developmental surveillance is supported at every health supervision visit, as is as the administration of standardized screening tests at the 9-, 18-, and 30-month visits. Developmental concerns elicited on surveillance at any visit should be followed by standardized developmental screening testing or direct referral to intervention and specialty medical care. Special attention to surveillance is recommended at the 4- to 5-year well-child visit, prior to entry into elementary education, with screening completed if there are any concerns. Developmental surveillance includes bidirectional communication with early childhood professionals in child care, preschools, Head Start, and other programs, including home visitation and parenting, particularly around developmental screening. The identification of problems should lead to developmental and medical evaluations, diagnosis, counseling, and treatment, in addition to early developmental intervention. Children with diagnosed developmental disorders are identified as having special health care needs, with initiation of chronic condition management in the pediatric medical home.
Although exaggerated host immune responses have been implicated in influenza-induced lung pathogenesis, the etiologic factors that contribute to these events are not completely understood. We ...previously demonstrated that neutrophil extracellular traps exacerbate pulmonary injury during influenza pneumonia. Histones are the major protein components of neutrophil extracellular traps and are known to have cytotoxic effects. Here, we examined the role of extracellular histones in lung pathogenesis during influenza. Mice infected with influenza virus displayed high accumulation of extracellular histones, with widespread pulmonary microvascular thrombosis. Occluded pulmonary blood vessels with vascular thrombi often exhibited endothelial necrosis surrounded by hemorrhagic effusions and pulmonary edema. Histones released during influenza induced cytotoxicity and showed strong binding to platelets within thrombi in infected mouse lungs. Nasal wash samples from influenza-infected patients also showed increased accumulation of extracellular histones, suggesting a possible clinical relevance of elevated histones in pulmonary injury. Although histones inhibited influenza growth in vitro, in vivo treatment with histones did not yield antiviral effects and instead exacerbated lung pathology. Blocking with antihistone antibodies caused a marked decrease in lung pathology in lethal influenza–challenged mice and improved protection when administered in combination with the antiviral agent oseltamivir. These findings support the pathogenic effects of extracellular histones in that pulmonary injury during influenza was exacerbated. Targeting histones provides a novel therapeutic approach to influenza pneumonia.
Physical function declines in old age, portending disability, increased health expenditures, and mortality. Cellular senescence, leading to tissue dysfunction, may contribute to these consequences of ...aging, but whether senescence can directly drive age-related pathology and be therapeutically targeted is still unclear. Here we demonstrate that transplanting relatively small numbers of senescent cells into young mice is sufficient to cause persistent physical dysfunction, as well as to spread cellular senescence to host tissues. Transplanting even fewer senescent cells had the same effect in older recipients and was accompanied by reduced survival, indicating the potency of senescent cells in shortening health- and lifespan. The senolytic cocktail, dasatinib plus quercetin, which causes selective elimination of senescent cells, decreased the number of naturally occurring senescent cells and their secretion of frailty-related proinflammatory cytokines in explants of human adipose tissue. Moreover, intermittent oral administration of senolytics to both senescent cell-transplanted young mice and naturally aged mice alleviated physical dysfunction and increased post-treatment survival by 36% while reducing mortality hazard to 65%. Our study provides proof-of-concept evidence that senescent cells can cause physical dysfunction and decreased survival even in young mice, while senolytics can enhance remaining health- and lifespan in old mice.
Raised peatlands, or bogs, are gently mounded landforms that are composed entirely of organic matter
and store the most carbon per area of any terrestrial ecosystem
. The shapes of bogs are ...critically important because their domed morphology
accounts for much of the carbon that bogs store and determines how they will respond to interventions
to stop greenhouse gas emissions and fires after anthropogenic drainage
. However, a general theory to infer the morphology of bogs is still lacking
. Here we show that an equation based on the processes universal to bogs explains their morphology across biomes, from Alaska, through the tropics, to New Zealand. In contrast to earlier models of bog morphology that attempted to describe only long-term equilibrium shapes
and were, therefore, inapplicable to most bogs
, our approach makes no such assumption and makes it possible to infer full shapes of bogs from a sample of elevations, such as a single elevation transect. Our findings provide a foundation for quantitative inference about the morphology, hydrology and carbon storage of bogs through Earth's history, as well as a basis for planning natural climate solutions by rewetting damaged bogs around the world.
Protein-based, fluorescent biosensors power basic research on cell signaling in health and disease, but their use in automated laboratories is limited. We have now created two live-cell assays, one ...for diacyl glycerol and another for cAMP, that are robust (Z′ > 0.7) and easily deployed on standard fluorescence plate readers. We describe the development of these assays, focusing on the parameters that were critical for optimization, in the hopes that the lessons learned can be generalized to the development of new biosensor-based assays.
Abstract
We search for an isotropic stochastic gravitational-wave background (GWB) in the 12.5 yr pulsar-timing data set collected by the North American Nanohertz Observatory for Gravitational Waves. ...Our analysis finds strong evidence of a stochastic process, modeled as a power law, with common amplitude and spectral slope across pulsars. Under our fiducial model, the Bayesian posterior of the amplitude for an
f
−2/3
power-law spectrum, expressed as the characteristic GW strain, has median 1.92 × 10
−15
and 5%–95% quantiles of 1.37–2.67 × 10
−15
at a reference frequency of
f
yr
=
1
yr
−
1
;
the Bayes factor in favor of the common-spectrum process versus independent red-noise processes in each pulsar exceeds 10,000. However, we find no statistically significant evidence that this process has quadrupolar spatial correlations, which we would consider necessary to claim a GWB detection consistent with general relativity. We find that the process has neither monopolar nor dipolar correlations, which may arise from, for example, reference clock or solar system ephemeris systematics, respectively. The amplitude posterior has significant support above previously reported upper limits; we explain this in terms of the Bayesian priors assumed for intrinsic pulsar red noise. We examine potential implications for the supermassive black hole binary population under the hypothesis that the signal is indeed astrophysical in nature.
Numerous studies are exploring the use of cell adoptive therapies to treat hematological malignancies as well as solid tumors. However, there are numerous factors that dampen the immune response, ...including viruses like human immunodeficiency virus. In this study, we leverage human-derived microphysiological models to reverse-engineer the HIV-immune system interaction and evaluate the potential of memory-like natural killer cells for HIV
head and neck cancer, one of the most common tumors in patients living with human immunodeficiency virus. Here, we evaluate multiple aspects of the memory-like natural killer cell response in human-derived bioengineered environments, including immune cell extravasation, tumor penetration, tumor killing, T cell dependence, virus suppression, and compatibility with retroviral medication. Overall, these results suggest that memory-like natural killer cells are capable of operating without T cell assistance and could simultaneously destroy head and neck cancer cells as well as reduce viral latency.
X-ray nanotomography is a powerful tool for the characterization of nanoscale materials and structures, but it is difficult to implement due to the competing requirements of X-ray flux and spot size. ...Due to this constraint, state-of-the-art nanotomography is predominantly performed at large synchrotron facilities. We present a laboratory-scale nanotomography instrument that achieves nanoscale spatial resolution while addressing the limitations of conventional tomography tools. The instrument combines the electron beam of a scanning electron microscope (SEM) with the precise, broadband X-ray detection of a superconducting transition-edge sensor (TES) microcalorimeter. The electron beam generates a highly focused X-ray spot on a metal target held micrometers away from the sample of interest, while the TES spectrometer isolates target photons with a high signal-to-noise ratio. This combination of a focused X-ray spot, energy-resolved X-ray detection, and unique system geometry enables nanoscale, element-specific X-ray imaging in a compact footprint. The proof of concept for this approach to X-ray nanotomography is demonstrated by imaging 160 nm features in three dimensions in six layers of a Cu-SiO
integrated circuit, and a path toward finer resolution and enhanced imaging capabilities is discussed.
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