Search results for "Base"

A motif-independent metric for DNA sequence specificity

2011

Abstract Background Genome-wide mapping of protein-DNA interactions has been widely used to investigate biological functions of the genome. An important question is to what extent such interactions are regulated at the DNA sequence level. However, current investigation is hampered by the lack of computational methods for systematic evaluating sequence specificity. Results We present a simple, unbiased quantitative measure for DNA sequence specificity called the Motif Independent Measure (MIM). By analyzing both simulated and real experimental data, we found that the MIM measure can be used to detect sequence specificity independent of presence of transcription factor (TF) binding motifs. We…

Identification of biomarkers in wastewater-based epidemiology: Main approaches and analytical methods

2021

Wastewater-based epidemiology (WBE) has become popular to estimate the use of drugs of abuse and recently to establish the incidence of CoVID 19 in large cities. However, its possibilities have been expanded recently as a technique that allows to establish a fingerprint of the characteristics of a city, such as state of health/disease, healthy/unhealthy living habits, exposure to different types of contaminants, etc. with respect to other cities. This has been thanks to the identification of human biomarkers as well as to the fingerprinting and profiling of the characteristics of the wastewater catchment that determine these circumstances. The purpose of this review is to analyze the differ…

Electrochemical probe for the monitoring of DNA-protein interactions.

2010

Self-assembly of thiol-terminated oligonucleotides on gold substrates provides a convenient way for DNA-functionalized surfaces. Here we describe the development of an electrochemical assay for the detection of DNA-protein interactions based on the modification of the electrochemical response of methylene blue (MB) intercalated in the DNA strands. Using a functionalized electrode with double stranded DNA carrying T3 RNA polymerase binding sequence, we show a substantial attenuation of the current upon the DNA-protein interaction. Moreover, a Langmuir binding isotherm for T3 RNA polymerase (T3 Pol) gives a dissociation constant K(D) equal to 0.46+/-0.23 microM. Such value is 100 times lower …

EVpedia: a community web portal for extracellular vesicles research

2014

Abstract Motivation: Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. Results: We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more tha…

The rise of the middle author: Investigating collaboration and division of labor in biomedical research using partial alphabetical authorship

2017

Contemporary biomedical research is performed by increasingly large teams. Consequently, an increasingly large number of individuals are being listed as authors in the bylines, which complicates the proper attribution of credit and responsibility to individual authors. Typically, more importance is given to the first and last authors, while it is assumed that the others (the middle authors) have made smaller contributions. However, this may not properly reflect the actual division of labor because some authors other than the first and last may have made major contributions. In practice, research teams may differentiate the main contributors from the rest by using partial alphabetical author…

Analysis of Production, Impact, and Scientific Collaboration on Difficult Airway Through the Web of Science and Scopus (1981-2013).

2017

Bibliometrics, the statistical analysis of written publications, is an increasingly popular approach to the assessment of scientific activity. Bibliometrics allows researchers to assess the impact of a field, or research area, and has been used to make decisions regarding research funding. Through bibliometric analysis, we hypothesized that a bibliometric analysis of difficult airway research would demonstrate a growth in authors and articles over time.Using the Web of Science (WoS) and Scopus databases, we conducted a search of published manuscripts on the difficult airway from January 1981 to December 2013. After removal of duplicates, we identified 2412 articles. We then analyzed the art…

BED: A new dataset for EEG-based biometrics

2021

Various recent research works have focused on the use of electroencephalography (EEG) signals in the field of biometrics. However, advances in this area have somehow been limited by the absence of a common testbed that would make it possible to easily compare the performance of different proposals. In this work, we present a data set that has been specifically designed to allow researchers to attempt new biometric approaches that use EEG signals captured by using relatively inexpensive consumer-grade devices. The proposed data set has been made publicly accessible and can be downloaded from https://doi.org/10.5281/zenodo.4309471 . It contains EEG recordings and responses from 21 individuals…

Minireview: pH and synaptic transmission

2013

AbstractAs a general rule a rise in pH increases neuronal activity, whereas it is dampened by a fall of pH. Neuronal activity per se also challenges pH homeostasis by the increase of metabolic acid equivalents. Moreover, the negative membrane potential of neurons promotes the intracellular accumulation of protons. Synaptic key players such as glutamate receptors or voltage-gated calcium channels show strong pH dependence and effects of pH gradients on synaptic processes are well known. However, the processes and mechanisms that allow controlling the pH in synaptic structures and how these mechanisms contribute to normal synaptic function are only beginning to be resolved.

Biopolyester-based systems containing naturally occurring compounds suitable for biomedical devices

2016

Novel bile acid conjugates with aryl/alkenyl linker: Synthesis and characterization

2008

Abstract Eight potential precursors for the design of bile acid derived receptors viz. 2,6-bis[dimethyl(3α-hydroxy-5β-cholan-24-amidoethyl)ammonio-methyl]naphthalene dibromide (1), 3,3′-bis[dimethyl(3α-hydroxy-5β-cholan-24-amidoethyl)ammoniomethyl]biphenyl dibromide (2), 3,3′-bis[dimethyl(3α,7α,12α-trihydroxy-5β-cholan-24-amidoethyl)ammoniomethyl]biphenyl dibromide (3), 4,4′-bis[dimethyl(3α-hydroxy-5β-cholan-24-amidoethyl)ammoniomethyl]stilbene dibromide (4), 4,4′-bis[dimethyl(3α,7α,12α-trihydroxy-5β-cholan-24-amidoethyl)ammoniomethyl]stilbene dibromide (5), allyl-dimethyl(3α,7α,12α-trihydroxy-5β-cholan-24-amidoethyl)ammonium bromide (6), 1,4′-bis[dimethyl(3α-hydroxy-5β-cholan-24-amidoethyl…