513 research outputs found
Effect of pooling samples on the efficiency of comparative studies using microarrays
Many biomedical experiments are carried out by pooling individual biological
samples. However, pooling samples can potentially hide biological variance and
give false confidence concerning the data significance. In the context of
microarray experiments for detecting differentially expressed genes, recent
publications have addressed the problem of the efficiency of sample-pooling,
and some approximate formulas were provided for the power and sample size
calculations. It is desirable to have exact formulas for these calculations and
have the approximate results checked against the exact ones. We show that the
difference between the approximate and exact results can be large. In this
study, we have characterized quantitatively the effect of pooling samples on
the efficiency of microarray experiments for the detection of differential gene
expression between two classes. We present exact formulas for calculating the
power of microarray experimental designs involving sample pooling and technical
replications. The formulas can be used to determine the total numbers of arrays
and biological subjects required in an experiment to achieve the desired power
at a given significance level. The conditions under which pooled design becomes
preferable to non-pooled design can then be derived given the unit cost
associated with a microarray and that with a biological subject. This paper
thus serves to provide guidance on sample pooling and cost effectiveness. The
formulation in this paper is outlined in the context of performing microarray
comparative studies, but its applicability is not limited to microarray
experiments. It is also applicable to a wide range of biomedical comparative
studies where sample pooling may be involved.Comment: 8 pages, 1 figure, 2 tables; to appear in Bioinformatic
Measuring the spatial and temporal pressure variation from buried charges
The effect of changing geotechnical parameters on the impulse generated from a shallow buried charge has been the topic of a large amount of scientific interest in recent years. Many previous researchers have utilised a free flying mass experimental approach to capture the impulse imparted from such an event. This methodology has also been used for a parametric study conducted at the University of Sheffield Blast and Impact laboratory A new approach which aims to better capture the loading from shallow buried charges uses a fixed plate with data recorded via load transducers and spatially and temporally resolved via an array of Hopkinson pressure bars. This paper outlines the revised experimental approach for the capture of spatially and temporally resolved impulse data at the blast-target interface. Issues encountered during the commissioning tests using charges bur-ied in silica sand are discussed, and initial results from the original and revised Hopkinson pressure bar arrays are presented
Urban tourism and population change: Gentrification in the age of mobilities
The prepandemic unbridled growth of tourism has triggered a significant debate
regarding the future of cities; several authors suggest that neighbourhood change
produced by tourism should be conceived as a form of gentrification. Yet research on
population shifts—a fundamental dimension of gentrification—in such
neighbourhoods is scarce. Our exploration of the Gòtic area in Barcelona, using quantitative
and qualitative techniques, reveals a process of population restructuring
characterised by a decrease of long-term residents and inhabited dwellings, and the
arrival of young and transnational gentrifiers that are increasingly mobile and form a
transient population. We then use some insights from the mobilities literature to
make sense of these results. In the gentrification of the Gòtic, the attractiveness of
the area for visitors and for a wider palette of transnational dwellers feeds one
another, resulting in an uneven negotiation whereby more wealthy and ‘footloose’
individuals gain access and control of space and housing over less mobile and more
dependent populations.info:eu-repo/semantics/publishedVersio
Multi-Method Characterisation of the Human Circulating Microbiome
The term microbiome describes the genetic material encoding the various microbial populations that inhabit our body. Whilst colonization of various body niches (e.g., the gut) by dynamic communities of microorganisms is now universally accepted, the existence of microbial populations in other “classically sterile” locations, including the blood, is a relatively new concept. The presence of bacteria-specific DNA in the blood has been reported in the literature for some time, yet the true origin of this is still the subject of much deliberation. The aim of this study was to investigate the phenomenon of a “blood microbiome” by providing a comprehensive description of bacterially derived nucleic acids using a range of complementary molecular and classical microbiological techniques. For this purpose we utilized a set of plasma samples from healthy subjects (n = 5) and asthmatic subjects (n = 5). DNA-level analyses involved the amplification and sequencing of the 16S rRNA gene. RNA-level analyses were based upon the de novo assembly of unmapped mRNA reads and subsequent taxonomic identification. Molecular studies were complemented by viability data from classical aerobic and anaerobic microbial culture experiments. At the phylum level, the blood microbiome was predominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key phyla detected were consistent irrespective of molecular method (DNA vs. RNA), and consistent with the results of other published studies. In silico comparison of our data with that of the Human Microbiome Project revealed that members of the blood microbiome were most likely to have originated from the oral or skin communities. To our surprise, aerobic and anaerobic cultures were positive in eight of out the ten donor samples investigated, and we reflect upon their source. Our data provide further evidence of a core blood microbiome, and provide insight into the potential source of the bacterial DNA/RNA detected in the blood. Further, data reveal the importance of robust experimental procedures, and identify areas for future consideration
Multi-Method Characterisation of the Human Circulating Microbiome
The term microbiome describes the genetic material encoding the various microbial populations that inhabit our body. Whilst colonization of various body niches (e.g., the gut) by dynamic communities of microorganisms is now universally accepted, the existence of microbial populations in other “classically sterile” locations, including the blood, is a relatively new concept. The presence of bacteria-specific DNA in the blood has been reported in the literature for some time, yet the true origin of this is still the subject of much deliberation. The aim of this study was to investigate the phenomenon of a “blood microbiome” by providing a comprehensive description of bacterially derived nucleic acids using a range of complementary molecular and classical microbiological techniques. For this purpose we utilized a set of plasma samples from healthy subjects (n = 5) and asthmatic subjects (n = 5). DNA-level analyses involved the amplification and sequencing of the 16S rRNA gene. RNA-level analyses were based upon the de novo assembly of unmapped mRNA reads and subsequent taxonomic identification. Molecular studies were complemented by viability data from classical aerobic and anaerobic microbial culture experiments. At the phylum level, the blood microbiome was predominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key phyla detected were consistent irrespective of molecular method (DNA vs. RNA), and consistent with the results of other published studies. In silico comparison of our data with that of the Human Microbiome Project revealed that members of the blood microbiome were most likely to have originated from the oral or skin communities. To our surprise, aerobic and anaerobic cultures were positive in eight of out the ten donor samples investigated, and we reflect upon their source. Our data provide further evidence of a core blood microbiome, and provide insight into the potential source of the bacterial DNA/RNA detected in the blood. Further, data reveal the importance of robust experimental procedures, and identify areas for future consideration
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Screening patients for unintentional carbon monoxide exposure in the Emergency Department: a cross-sectional multi-centre study.
BACKGROUND: Low-level exposure to carbon monoxide (CO) is a significant health concern but is difficult to diagnose. This main study aim was to establish the prevalence of low-level CO poisoning in Emergency Department (ED) patients. METHODS: A prospective cross-sectional study of patients with symptoms of CO exposure was conducted in four UK EDs between December 2018 and March 2020. Data on symptoms, a CO screening tool and carboxyhaemoglobin were collected. An investigation of participants' homes was undertaken to identify sources of CO exposure. RESULTS: Based on an ED assessment of 4175 participants, the prevalence of suspected CO exposure was 0.62% (95% CI; 0.41-0.91%). CO testing in homes confirmed 1 case of CO presence and 21 probable cases. Normal levels of carboxyhaemoglobin were found in 19 cases of probable exposure and in the confirmed case. CONCLUSION: This study provides evidence that ED patients with symptoms suggestive of CO poisoning but no history of CO exposure are at risk from CO poisoning. The findings suggest components of the CO screening tool may be an indicator of CO exposure over and above elevated COHb. Clinicians should have a high index of suspicion for CO exposure so that this important diagnosis is not missed
Effects of Long-Term Pioglitazone Treatment on Peripheral and Central Markers of Aging
BACKGROUND: Thiazolidinediones (TZDs) activate peroxisome proliferator-activated receptor gamma (PPARgamma) and are used clinically to help restore peripheral insulin sensitivity in Type 2 diabetes (T2DM). Interestingly, long-term treatment of mouse models of Alzheimer\u27s disease (AD) with TZDs also has been shown to reduce several well-established brain biomarkers of AD including inflammation, oxidative stress and Abeta accumulation. While TZD\u27s actions in AD models help to elucidate the mechanisms underlying their potentially beneficial effects in AD patients, little is known about the functional consequences of TZDs in animal models of normal aging. Because aging is a common risk factor for both AD and T2DM, we investigated whether the TZD, pioglitazone could alter brain aging under non-pathological conditions.
METHODS AND FINDINGS: We used the F344 rat model of aging, and monitored behavioral, electrophysiological, and molecular variables to assess the effects of pioglitazone (PIO-Actos® a TZD) on several peripheral (blood and liver) and central (hippocampal) biomarkers of aging. Starting at 3 months or 17 months of age, male rats were treated for 4-5 months with either a control or a PIO-containing diet (final dose approximately 2.3 mg/kg body weight/day). A significant reduction in the Ca2+-dependent afterhyperpolarization was seen in the aged animals, with no significant change in long-term potentiation maintenance or learning and memory performance. Blood insulin levels were unchanged with age, but significantly reduced by PIO. Finally, a combination of microarray analyses on hippocampal tissue and serum-based multiplex cytokine assays revealed that age-dependent inflammatory increases were not reversed by PIO.
CONCLUSIONS: While current research efforts continue to identify the underlying processes responsible for the progressive decline in cognitive function seen during normal aging, available medical treatments are still very limited. Because TZDs have been shown to have benefits in age-related conditions such as T2DM and AD, our study was aimed at elucidating PIO\u27s potentially beneficial actions in normal aging. Using a clinically-relevant dose and delivery method, long-term PIO treatment was able to blunt several indices of aging but apparently affected neither age-related cognitive decline nor peripheral/central age-related increases in inflammatory signaling
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