270 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
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
Airbnb and crime in Barcelona (Spain): testing the relationship using a geographically weighted regression
The existence of works proving the possible relationship empirically that Airbnb lodgings could have with crime in Spain is not known. This research analyzes the relationship between Airbnb lodgings and crimes against the properties and people in Barcelona’s neighbourhoods. To achieve this, we use an ordinary least squares regression model and a geographically weighted regression model. The results show a significant and positive relationship between the higher density of Airbnb lodgings and the higher crime rates in the neighbourhoods, especially of patrimonial nature. Divided by type of leased space, the Airbnb homes, in which the guest shares a room with other guests, show a higher relationship with crimes against property and people. The results of the local model show a spatial heterogeneity in all variables used, indicating the need to address non-stationary spatial processes that reveal hidden patterns. However, the only variable that shows statistically significant local variability is the total Airbnb lodgings variable. Finally, we discussed some unexpected results, proposing some future lines of research. © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Nanjing Normal University
Thermoregulation and fluid balance during a 30-km march in 60-versus 80-year-old subjects
The presence of impaired thermoregulatory and fluid balance responses to exercise in older individuals is well established. To improve our understanding on thermoregulation and fluid balance during exercise in older individuals, we compared thermoregulatory and fluid balance responses between sexagenarians and octogenarians during prolonged exercise. Forty sexagenarians (60 ± 1 year) and 36 octogenarians (81 ± 2 year) volunteered to participate in a 30-km march at a self-selected pace. Intestinal temperature (T in) and heart rate were recorded every 5 km. Subjects reported fluid intake, while urine output was measured and sweat rate was calculated. Octogenarians demonstrated a lower baseline T in and a larger exercise-induced increase in T in compared to sexagenarians (1.2 ± 0.5 °C versus 0.7 ± 0.4 °C, p 0.05). These results suggest that thermoregulatory responses deteriorate with advancing age, while fluid balance is regulated appropriately during a 30-km walking march under moderate ambient conditions
Embryonic and adult isoforms of XLAP2 form microdomains associated with chromatin and the nuclear envelope
Laminin-associated polypeptide 2 (LAP2) proteins are alternatively spliced products of a single gene; they belong to the LEM domain family and, in mammals, locate to the nuclear envelope (NE) and nuclear lamina. Isoforms lacking the transmembrane domain also locate to the nucleoplasm. We used new specific antibodies against the N-terminal domain of Xenopus LAP2 to perform immunoprecipitation, identification and localization studies during Xenopus development. By immunoprecipitation and mass spectrometry (LC/MS/MS), we identified the embryonic isoform XLAP2γ, which was downregulated during development similarly to XLAP2ω. Embryonic isoforms XLAP2ω and XLAP2γ were located in close association with chromatin up to the blastula stage. Later in development, both embryonic isoforms and the adult isoform XLAP2β were localized in a similar way at the NE. All isoforms colocalized with lamin B2/B3 during development, whereas XLAP2β was colocalized with lamin B2 and apparently with the F/G repeat nucleoporins throughout the cell cycle in adult tissues and culture cells. XLAP2β was localized in clusters on chromatin, both at the NE and inside the nucleus. Embryonic isoforms were also localized in clusters at the NE of oocytes. Our results suggest that XLAP2 isoforms participate in the maintenance and anchoring of chromatin domains to the NE and in the formation of lamin B microdomains
Oxidation of DJ-1 Induced by 6-Hydroxydopamine Decreasing Intracellular Glutathione
DJ-1, the causative gene of a familial form of Parkinson's disease (PD), has been reported to undergo preferential oxidation of the cysteine residue at position 106 (Cys-106) under oxidative stress; however, details of the molecular mechanisms are not well known. In the present study, mechanisms of DJ-1 oxidation induced by 6-hydroxydopamine (6-OHDA) were investigated by using SH-SY5Y cells. The treatment of these cells with 6-OHDA caused an obvious acidic spot sift of DJ-1 due to its oxidation. However, when catalase, which is an hydrogen peroxide (H2O2)-removing enzyme, was added during the treatment, it failed to prevent the oxidation induced by 6-OHDA, suggesting that electrophilic p-quinone formed from 6-OHDA, but not H2O2, was responsible for the DJ-1 oxidation. Benzoquinone, another electrophilic p-quinone, also induced DJ-1 oxidation. The intracellular glutathione (GSH) levels were significantly decreased by 6-OHDA, irrespective of the presence or absence of catalase. The inhibition of GSH synthesis by buthionine sulfoximine resulted in a decrease in GSH levels and enhancement of DJ-1 oxidation. The pretreatment of cells with N-acetyl-cysteine prevented the loss of intracellular GSH and subsequently DJ-1 oxidation induced by 6-OHDA. Collectively, these results suggest that electrophilic p-quinone formed from 6-OHDA induces DJ-1 oxidation by decreasing intracellular GSH
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