Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) ...Consortium, we apply a reproducible, cloud-based pipeline to integrate multiple short- and linked-read sequencing datasets and provide benchmark calls for human genomes. We generate benchmark calls for one previously analyzed GIAB sample, as well as six genomes from the Personal Genome Project. These new genomes have broad, open consent, making this a 'first of its kind' resource that is available to the community for multiple downstream applications. We produce 17% more benchmark single nucleotide variations, 176% more indels and 12% larger benchmark regions than previously published GIAB benchmarks. We demonstrate that this benchmark reliably identifies errors in existing callsets and highlight challenges in interpreting performance metrics when using benchmarks that are not perfect or comprehensive. Finally, we identify strengths and weaknesses of callsets by stratifying performance according to variant type and genome context.
Weight loss from calorie restriction (CR) and/or endurance exercise training (EX) is cardioprotective. However CR and EX also have weight loss-independent benefits.
We tested the hypothesis that ...weight loss from calorie restriction and exercise combined (CREX) improves cardiovascular disease (CVD) risk factors more so than similar weight loss from CR or EX alone.
Overweight, sedentary men and women (n = 52; aged 45-65 y) were randomly assigned to undergo 6-8% weight loss by using CR, EX, or CREX. Outcomes were measured before and after weight loss and included maximal oxygen consumption (VO2max), resting blood pressure, fasting plasma lipids, glucose, C-reactive protein, and arterial stiffness carotid-femoral pulse wave velocity (PWV) and carotid augmentation index (AI). Values are means ± SEs.
Reductions in body weight (∼7%) were similar in all groups. VO2max changed in proportion to the amount of exercise performed (CR, -1% ± 3%; EX, +22% ± 3%; and CREX, +11% ± 3%). None of the changes in CVD risk factors differed between groups. For all groups combined, decreases were observed for systolic and diastolic blood pressure (-5 ± 1 and -4 ± 1 mm Hg, respectively; both P < 0.0008), total cholesterol (-17 ± 4 mg/dL; P < 0.0001), non-HDL cholesterol (-16 ± 3 mg/dL; P < 0.0001), triglycerides (-18 ± 8 mg/dL; P = 0.03), and glucose (-3 ± 1 mg/dL; P = 0.0003). No changes were observed for HDL cholesterol (P = 0.30), C-reactive protein (P = 0.10), PWV (P = 0.30), or AI (P = 0.84). These changes would be expected to decrease the lifetime risk of CVD from 46% to 36%.
Matched weight losses from CR, EX, and CREX have substantial beneficial effects on CVD risk factors. However, the effects are not additive when weight loss is matched. This trial was registered at clinicaltrials.gov as NCT00777621.
Abstract
Pyrophytic oak landscapes across the central and eastern United States are losing dominance as shade-tolerant, fire-sensitive, or opportunistic tree species encroach into these ecosystems in ...the absence of periodic, low-intensity surface fires. Mesophication, a hypothesized process initiated by intentional fire exclusion by which these encroaching species progressively create conditions favorable for their own persistence at the expense of pyrophytic species, is commonly cited as causing this structural and compositional transition. However, many questions remain regarding mesophication and its role in declining oak dominance. In the present article, we review support and key knowledge gaps for the mesophication hypothesis. We then pose avenues for future research that consider which tree species and tree traits create self-perpetuating conditions and under what conditions tree-level processes might affect forest flammability at broader scales. Our goal is to promote research that can better inform restoration and conservation of oak ecosystems experiencing structural and compositional shifts across the region.
Abstract Tissue engineering strategies that primarily use biological extracellular matrices (ECMs) with or without the inclusion of a stem or progenitor cell source are under development for the ...treatment of trauma resulting in the loss of a large volume of skeletal muscle (i.e., volumetric muscle loss; VML). The explicit goal is to restore functional capacity to the injured tissue by promoting generation of muscle fibers. In the current study, a syngeneic muscle-derived ECM (mECM) was transplanted in a rat tibialis anterior (TA) muscle VML model. Instead of muscle fiber generation a large fibrotic mass was produced by mECM transplantation out to six months post-injury. Surprisingly, recovery of one-third of the original functional deficit was still achieved by two months post-injury following mECM transplantation. These counterintuitive findings may be due, at least in part, to the ability of mECM to attenuate muscle damage in the remaining muscle as compared to non-repaired muscle. These findings point to a novel role of biological ECMs for the treatment of VML, wherein the remaining muscle mass is protected from prolonged overload injury.
Cell Therapies for Acute Radiation Syndrome Christy, Barbara A.; Herzig, Maryanne C.; Wu, Xiaowu ...
International journal of molecular sciences,
06/2024, Volume:
25, Issue:
13
Journal Article
Peer reviewed
Open access
The risks of severe ionizing radiation exposure are increasing due to the involvement of nuclear powers in combat operations, the increasing use of nuclear power, and the existence of terrorist ...threats. Exposure to a whole-body radiation dose above about 0.7 Gy results in H-ARS (hematopoietic acute radiation syndrome), which is characterized by damage to the hematopoietic system; higher doses result in further damage to the gastrointestinal and nervous systems. Only a few medical countermeasures for ARS are currently available and approved for use, although others are in development. Cell therapies (cells or products produced by cells) are complex therapeutics that show promise for the treatment of radiation injury and have been shown to reduce mortality and morbidity in animal models. Since clinical trials for ARS cannot be ethically conducted, animal testing is extremely important. Here, we describe cell therapies that have been tested in animal models. Both cells and cell products appear to promote survival and lessen tissue damage after whole-body irradiation, although the mechanisms are not clear. Because radiation exposure often occurs in conjunction with other traumatic injuries, animal models of combined injury involving radiation and future countermeasure testing for these complex medical problems are also discussed.
In read cloud approaches, microfluidic partitioning of long genomic DNA fragments and barcoding of shorter fragments derived from these fragments retains long-range information in short sequencing ...reads. This combination of short reads with long-range information represents a powerful alternative to single-molecule long-read sequencing. We develop Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs) for SV detection and assembly from read cloud data and apply this method to Illumina-sequenced 10x Genomics sarcoma and breast cancer data sets. Compared with short-fragment sequencing, GROC-SVs substantially improves the specificity of breakpoint detection at comparable sensitivity. This approach also performs sequence assembly across multiple breakpoints simultaneously, enabling the reconstruction of events exhibiting remarkable complexity. We show that chromothriptic rearrangements occurred before copy number amplifications, and that rates of single-nucleotide variants and SVs are not correlated. Our results support the use of read cloud approaches to advance the characterization of large and complex structural variation.
Abstract Stem cell response to a library of scaffolds with varied 3D structures was investigated. Microarray screening revealed that each type of scaffold structure induced a unique gene expression ...signature in primary human bone marrow stromal cells (hBMSCs). Hierarchical cluster analysis showed that treatments sorted by scaffold structure and not by polymer chemistry suggesting that scaffold structure was more influential than scaffold composition. Further, the effects of scaffold structure on hBMSC function were mediated by cell shape. Of all the scaffolds tested, only scaffolds with a nanofibrous morphology were able to drive the hBMSCs down an osteogenic lineage in the absence of osteogenic supplements. Nanofiber scaffolds forced the hBMSCs to assume an elongated, highly branched morphology. This same morphology was seen in osteogenic controls where hBMSCs were cultured on flat polymer films in the presence of osteogenic supplements (OS). In contrast, hBMSCs cultured on flat polymer films in the absence of OS assumed a more rounded and less-branched morphology. These results indicate that cells are more sensitive to scaffold structure than previously appreciated and suggest that scaffold efficacy can be optimized by tailoring the scaffold structure to force cells into morphologies that direct them to differentiate down the desired lineage.
Highlights • EHR use appears to improve capture of patient biomedical information. • EHR use may interfere with nonverbal engagement between patients and physicians. • EHR use may interfere with ...capture of psychosocial and emotional information. • Patient access and use of EHR may increase engagement and self-management.
Summary
The dead foliage of scorched crowns is one of the most conspicuous signatures of wildland fires. Globally, crown scorch from fires in savannas, woodlands and forests causes tree stress and ...death across diverse taxa. The term crown scorch, however, is inconsistently and ambiguously defined in the literature, causing confusion and conflicting interpretation of results. Furthermore, the underlying mechanisms causing foliage death from fire are poorly understood. The consequences of crown scorch – alterations in physiological, biogeochemical and ecological processes and ecosystem recovery pathways – remain largely unexamined. Most research on the topic assumes the mechanism of leaf and bud death is exposure to lethal air temperatures, with few direct measurements of lethal heating thresholds. Notable information gaps include how energy transfer injures and kills leaves and buds, how nutrients, carbohydrates, and hormones respond, and what physiological consequences lead to mortality. We clarify definitions to encourage use of unified terminology for foliage and bud necrosis resulting from fire. We review the current understanding of the physical mechanisms driving foliar injury, discuss the physiological responses, and explore novel ecological consequences of crown injury from fire. From these elements, we propose research needs for the increasingly interdisciplinary study of fire effects.
Early post injury mitigation strategies in ARDS are in short supply. Treatments with allogeneic stromal cells are administered after ARDS develops, require specialized expertise and equipment, and to ...date have shown limited benefit.
Assess the efficacy of immediate post injury intravenous administration of autologous or allogeneic bone marrow-derived mesenchymal stromal cells (MSCs) for the treatment of acute respiratory distress syndrome (ARDS) due to smoke inhalation and burns.
Yorkshire swine (
= 32, 44.3 ± 0.5 kg) underwent intravenous anesthesia, placement of lines, severe smoke inhalation, and 40% total body surface area flame burns, followed by 72 hours of around-the-clock ICU care. Mechanical ventilation, fluids, pressors, bronchoscopic cast removal, daily lung computed tomography scans, and arterial blood assays were performed. After injury and 24 and 48 hours later, animals were randomized to receive autologous concentrated bone marrow aspirate (
= 10; 3 × 10
white blood cells and a mean of 56.6 × 10
platelets per dose), allogeneic MSCs (
= 10; 6.1 × 10
MSCs per dose) harvested from healthy donor swine, or no treatment in injured control animals (
= 12).
The intravenous administration of MSCs after injury and at 24 and 48 hours delayed the onset of ARDS in swine treated with autologous MSCs (48 ± 10 h) versus control animals (14 ± 2 h) (
= 0.004), reduced ARDS severity at 24 (
< 0.001) and 48 (
= 0.003) hours, and demonstrated visibly diminished consolidation on computed tomography (not significant). Mortality at 72 hours was 1 in 10 (10%) in the autologous group, 5 in 10 (50%) in the allogeneic group, and 6 in 12 (50%) in injured control animals (not significant). Both autologous and allogeneic MSCs suppressed systemic concentrations of TNF-α (tumor necrosis factor-α).
The intravenous administration of three doses of freshly processed autologous bone marrow-derived MSCs delays ARDS development and reduces its severity in swine. Bedside retrieval and administration of autologous MSCs in swine is feasible and may be a viable injury mitigation strategy for ARDS.
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