SNAD: sequence name annotation-based designer

<p>Abstract</p> <p>Background</p> <p>A growing diversity of biological data is tagged with unique identifiers (UIDs) associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions.</p> <p>Results</p> <p>Here we introduce SNAD (Sequence Name Annotation-based Designer) that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list) into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology.</p> <p>Conclusion</p> <p>A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.</p

Correlation between binding rate constants and individual information of E. coli Fis binding sites

Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics appear to be inaccessible from sequence information since the relative contributions of the on- and off-rates to the binding constant, and hence the free energy, are unknown. However, the on-rate could be independent of the sequence since a protein is likely to bind once it is near a site. To test this, we used surface plasmon resonance and electromobility shift assays to determine the kinetics for binding of the Fis protein to a range of naturally occurring binding sites. We observed that the logarithm of the off-rate is indeed proportional to the individual information of the binding sites, as predicted. However, the on-rate is also related to the information, but to a lesser degree. We suggest that the on-rate is mostly determined by DNA bending, which in turn is determined by the sequence information. Finally, we observed a break in the binding curve around zero bits of information. The break is expected from information theory because it represents the coding demarcation between specific and nonspecific binding

Wearable laser Doppler sensors for evaluating the nutritive and shunt blood flow

This study is devoted to the trials of wearable diagnostic system that implements the laser Doppler flowmetry technique to analyse the blood microcirculation. We do preliminary test with involvement of limited group of healthy volunteers of different age and in patients with type 2 diabetes. During the series of measurements, the microcirculation parameters was measured for 10 minutes in the palmar surfaces of the big toes and in the inner sides of the upper thirds of the shins. A statistically significant differences was found in bypass index, nutritive and shunt blood ow in shins between older group of volunteers and patients' group as well as in shunt blood flow in fingers between younger and older groups of volunteers

Studies of age-related changes in blood perfusion coherence using wearable blood perfusion sensor system

Laser Doppler flowmetry (LDF) was used for detection of age-related changes in the blood microcirculation. The LDF signal was simultaneously recorded from the 3rd fingers' pads of both hands. Amplitudes of the blood flow oscillations and wavelet coherence of the signals were used for the data analysis. A statistical difference in the synchronisation of myogenic oscillations was found between the two studied age groups. Myogenic oscillations of blood perfusion in the younger group had a higher wavelet coherence parameter than in the older group. Observed site-specific and age-related differences in blood perfusion can be used in the future in the design of experimental studies of the blood microcirculation system in patients with different pathologies

Wearable sensor system for multipoint measurements of blood perfusion: pilot studies in patients with diabetes mellitus

The growing interest in the development of new wearable electronic devices for mobile healthcare provides great opportunities for the development of methods for assessing blood perfusion in this direction. Laser Doppler flowmetry (LDF) is one of the promising methods. A fine analysis of capillary blood ow structure and rhythm in the time and frequency domains, coupled with a new possibility of round-the-clock monitoring can provide valuable diagnostic information about the state of microvascular blood ow. In this study, wearable implementation of laser Doppler flowmetry was utilised for microcirculatory function assessment in patients with diabetes and healthy controls of two distinct age groups. Four wearable laser Doppler flowmetry monitors were used for the analysis of blood microcirculation. Thirty-seven healthy volunteers and 18 patients with type 2 diabetes mellitus participated in the study. The results of the studies have shown that the average perfusion differs between healthy volunteers of distinct age groups and between healthy volunteers of the younger age group and patients with diabetes mellitus. It was noted that the average level of perfusion measured on the wrist in the two groups of healthy volunteers has no statistically significant differences found in similar measurements on the fingertips. The wearable implementation of LDF can become a truly new diagnostic interface to monitor cardiovascular parameters, which could be of interest for diagnostics of conditions associated with microvascular disorders

Laser Doppler flowmetry in blood and lymph monitoring, technical aspects and analysis

The aim of this work was to study the possibilities of the laser Doppler flowmetry method for the joint study of microhaemo- and lymph circulation of human skin. Conducting a series of experimental studies allowed to trace the relationship of recorded signals of microcirculation of blood flow and lymph flow, as well as to study their oscillation nature by using wavelet analysis

Novel wearable VCSEL-based sensors for multipoint measurements of blood perfusion

A novel non-invasive, wearable VCSEL-based system for multipoint in − vivo measurements of blood perfusion was introduced. The system operates on the basis of the laser Doppler flowmetry (LDF) method and allows for microcirculation studies. The sensors developed were used to analyse the skin blood flow synchronization in homologous regions of the contralateral limbs, both in the basal state and during various functional tests. A high synchronisation of blood flow rhythms in the contralateral limbs of healthy volunteers was shown in the studies presented

Electrical properties of optimized nBn structures based on HgCdTe grown by molecular beam epitaxy

The use of unipolar barrier architectures in infrared detectors based on HgCdTe grown by molecular beam epitaxy (MBE) provides significant technological advantages. Earlier, the authors of the manuscript presented the results of a study of dark currents [1] and admittance [2] of the first variants of MBE HgCdTe nBn structures. This paper presents the results of electrical characterization of nBn structures with parameters optimized for detection in the spectral ranges 3–5 (MWIR) and 8–12 (LWIR) µm

Wearable laser Doppler flowmetry for the analysis of microcirculatory changes during intravenous infusion in patients with diabetes mellitus

The article is aimed at conducting pilot studies of microcirculation changes in patients with diabetes mellitus during the course of intravenous infusions of alpha lipoic acid. The study was conducted with patients with diabetes during the passage of a standard course of treatment. The change in parameters was compared before the start of the infusion course, during and after the course. A system of wearable laser Doppler monitors was used to conduct the study. The study showed that although the microcirculation index does not undergo significant changes during the treatment process, spectral analysis of the recorded signal has potential applicability. Further studies with a larger sample group are required for a qualitative analysis of the observed effects