Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
864
result(s) for
"Campbell, Ross"
Sort by:
Accelerating genomic workflows using NVIDIA Parabricks
Background
As genome sequencing becomes better integrated into scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing these vast datasets. Although much work has been done to reduce compute times using various configurations of traditional CPU computing infrastructures, Graphics Processing Units (GPUs) offer opportunities to accelerate genomic workflows by orders of magnitude. Here we benchmark one GPU-accelerated software suite called NVIDIA Parabricks on Amazon Web Services (AWS), Google Cloud Platform (GCP), and an NVIDIA DGX cluster. We benchmarked six variant calling pipelines, including two germline callers (HaplotypeCaller and DeepVariant) and four somatic callers (Mutect2, Muse, LoFreq, SomaticSniper).
Results
We achieved up to 65 × acceleration with germline variant callers, bringing HaplotypeCaller runtimes down from 36 h to 33 min on AWS, 35 min on GCP, and 24 min on the NVIDIA DGX. Somatic callers exhibited more variation between the number of GPUs and computing platforms. On cloud platforms, GPU-accelerated germline callers resulted in cost savings compared with CPU runs, whereas some somatic callers were more expensive than CPU runs because their GPU acceleration was not sufficient to overcome the increased GPU cost.
Conclusions
Germline variant callers scaled well with the number of GPUs across platforms, whereas somatic variant callers exhibited more variation in the number of GPUs with the fastest runtimes, suggesting that, at least with the version of Parabricks used here, these workflows are less GPU optimized and require benchmarking on the platform of choice before being deployed at production scales. Our study demonstrates that GPUs can be used to greatly accelerate genomic workflows, thus bringing closer to grasp urgent societal advances in the areas of biosurveillance and personalized medicine.
Journal Article
لغات الحب الخمس التي يستخدمها الأطفال
أنت تعرف أنك تحب طفلك ولكن كيف تستطيع أن تظهر له هذا لكي يشعر حقا بأنه محبوب ؟ احتل هذا الكتاب قمة قائمة نيويورك تايمز للكاتب الأكثر مبيعا وقد ساعد الملايين من الأزواج على معرفة سر بناء حب يستمر والآن اكتشف كيفية الحديث بلغة حب طفلك واجعله يشعر بأنه محبوب بطريقة يفهمها واكتشف عشرات النصائح عن طرق عملية لتتحدث لغة حب طفلك.
BOOK
The Role of Ageing and Parenchymal Senescence on Macrophage Function and Fibrosis
In this review, we examine senescent cells and the overlap between the direct biological impact of senescence and the indirect impact senescence has via its effects on other cell types, particularly the macrophage. The canonical roles of macrophages in cell clearance and in other physiological functions are discussed with reference to their functions in diseases of the kidney and other organs. We also explore the translational potential of different approaches based around the macrophage in future interventions to target senescent cells, with the goal of preventing or reversing pathologies driven or contributed to in part by senescent cell load in vivo.
Journal Article
Gene expression profiling of whole blood: A comparative assessment of RNA-stabilizing collection methods
Peripheral Blood gene expression is widely used in the discovery of biomarkers and development of therapeutics. Recently, a spate of commercial blood collection and preservation systems have been introduced with proprietary variations that may differentially impact the transcriptomic profiles. Comparative analysis of these collection platforms will help optimize protocols to detect, identify, and reproducibly validate true biological variance among subjects. In the current study, we tested two recently introduced whole blood collection methods, RNAgard® and PAXgene® RNA, in addition to the traditional method of peripheral blood mononuclear cells (PBMCs) separated from whole blood and preserved in Trizol reagent. Study results revealed striking differences in the transcriptomic profiles from the three different methods that imply ex vivo changes in gene expression occurred during the blood collection, preservation, and mRNA extraction processes. When comparing the ability of the three preservation methods to accurately capture individuals' expression differences, RNAgard® outperformed PAXgene® RNA, and both showed better individual separation of transcriptomic profiles than PBMCs. Hence, our study recommends using a single blood collection platform, and strongly cautions against combining methods during the course of a defined study.
Journal Article
Severe, short-term sleep restriction reduces gut microbiota community richness but does not alter intestinal permeability in healthy young men
Sleep restriction alters gut microbiota composition and intestinal barrier function in rodents, but whether similar effects occur in humans is unclear. This study aimed to determine the effects of severe, short-term sleep restriction on gut microbiota composition and intestinal permeability in healthy adults. Fecal microbiota composition, measured by 16S rRNA sequencing, and intestinal permeability were measured in 19 healthy men (mean ± SD; BMI 24.4 ± 2.3 kg/m
2
, 20 ± 2 years) undergoing three consecutive nights of adequate sleep (AS; 7–9 h sleep/night) and restricted sleep (SR; 2 h sleep/night) in random order with controlled diet and physical activity. α-diversity measured by amplicon sequencing variant (ASV) richness was 21% lower during SR compared to AS (
P
= 0.03), but α-diversity measured by Shannon and Simpson indexes did not differ between conditions. Relative abundance of a single ASV within the family Ruminococcaceae was the only differentially abundant taxon (
q
= 0.20). No between-condition differences in intestinal permeability or β-diversity were observed. Findings indicated that severe, short-term sleep restriction reduced richness of the gut microbiota but otherwise minimally impacted community composition and did not affect intestinal permeability in healthy young men.
Journal Article
Multiomic analysis of human kidney disease identifies a tractable inflammatory and pro-fibrotic tubular cell phenotype
Maladaptive proximal tubular (PT) epithelial cells have been implicated in progression of chronic kidney disease (CKD), however the complexity of epithelial cell states within the fibrotic niche remains incompletely understood. Hence, we integrated snRNA and ATAC-seq with high-plex single-cell molecular imaging to generate a spatially-revolved multiomic atlas of human kidney disease. We demonstrate that in injured kidneys, a subset of
HAVCR1
+
VCAM1
+
PT cells acquired an inflammatory phenotype, upregulating genes encoding chemokines, pro-fibrotic and senescence-associated proteins and adhesion molecules including
ICAM1
. Spatial transcriptomic and multiplex-immunofluorescence determined that specifically these VCAM1
+
ICAM1
+
inflammatory PT cells localised to the fibrotic niche. Ligand-receptor analysis highlighted paracrine signaling from inflammatory PT cells mediating leucocyte recruitment and myofibroblast activation. Loss of HNF4α and activation of NF-κβ and AP-1 transcription factors epigenetically imprinted the inflammatory phenotype. Targeting inflammatory tubular cells by administering an AP-1 inhibitor or senolytic agent ameliorated inflammation and fibrosis in murine models of kidney injury, hence these cells may be a tractable target in CKD.
The complexity of epithelial cell states in the fibrotic niche in the context of chronic kidney disease remains incompletely understood. Here the authors integrate snRNA and ATAC-seq with high-plex single-cell molecular imaging to generate a spatially-revolved multiomic atlas of human kidney disease.
Journal Article
A prospective cohort study assessing the clinical utility of the Cottle maneuver in nasal septal surgery
Background
A nasal septal deviation can have a significant detrimental effect on a patient’s quality of life. Nasal valve collapse (NVC) often co-exists with a septal deviation. The Cottle maneuver is one of the most common methods to diagnose NVC; however, no study has assessed the efficacy of this physical exam finding. This study tests the hypothesis that patients with nasal obstruction due to a septal deviation with a negative pre-operative Cottle maneuver will demonstrate a greater improvement in their Nasal Obstruction Symptom Evaluation (NOSE) score, compared to patients who demonstrate a positive pre-operative Cottle maneuver, when assessed at 12 months following a septoplasty with turbinate diathermy.
Methods
This was a prospective Cohort Study. The population was 141 patients with nasal obstruction due to a septal deviation with or without nasal valve collapse, excluding patients with bilateral complete nasal valve collapse. Patients were placed in cohorts according to the results of the Cottle maneuver (positive or negative). A NOSE questionnaire was administered at baseline and 12-months after a septoplasty with turbinate diathermy. Non-adjusted NOSE scores were used (score out of 20). An ANOVA was used to compare if there was a difference in outcomes between patient cohorts.
Results
One hundred and forty-one patients completed 12-month follow-up with 71.5% of patients demonstrating a positive Cottle maneuver at baseline. The mean (95% C.I.) difference in NOSE score at 12 months between patients with a positive Cottle versus a negative Cottle was 0.18 (− 1.6 to 1.92;
p
= 0.38).
Conclusion
In a univariate, single surgeon study, a positive Cottle Maneuver does not appear to influence outcomes in the described patient population compared to those with a negative Cottle Maneuver when undergoing a septoplasty.
Journal Article
Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays
Background
Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questions: what collective patterns do most analytes follow, which analytes follow an identical pattern or synchronize across multiple cohorts, and how do biological functions evolve over time. Existing tools fall short of robustly answering and visualizing all three questions in a unified interface.
Results
Functional Heatmap offers time-series data visualization through a Master Panel page, and Combined page to answer each of the three time-series questions. It dissects the complex multi-omics time-series readouts into patterned clusters with associated biological functions. It allows users to identify a cascade of functional changes over a time variable. Inversely, Functional Heatmap can compare a pattern with specific biology respond to multiple experimental conditions. All analyses are interactive, searchable, and exportable in a form of heatmap, line-chart, or text, and the results are easy to share, maintain, and reproduce on the web platform.
Conclusions
Functional Heatmap is an automated and interactive tool that enables pattern recognition in time-series multi-omics assays. It significantly reduces the manual labour of pattern discovery and comparison by transferring statistical models into visual clues. The new pattern recognition feature will help researchers identify hidden trends driven by functional changes using multi-tissues/conditions on a time-series fashion from omic assays.
Journal Article