Image Analysis Workflow for 2-D Electrophoresis Gels Based on ImageJ

A number of commercial software packages are currently available to perform digital two-dimensional electrophoresis (2D-GE) gel analysis. However, both the high cost of the commercial packages and the unavailability of a standard data analysis workflow, have prompted several groups to develop freeware systems to perform certain steps of gel analysis. Unfortunately, to the best of our knowledge none of them offer a package that performs all the steps envisaged in a 2D-GE gel analysis. Here we describe an ImageJ-based procedure, able to manage all the steps of a 2D-GE gel analysis. ImageJ is a free available image processing and analysis application developed by National Institutes of Health (NIH) and widely used in different life sciences fields as medical imaging, microscopy, western blotting and PAGE. Nevertheless no one has yet developed a procedure enabled to compare spots on 2D-GE gels. We collected all used ImageJ tools in a plug-in that allows us to perform the whole 2D-GE analysis. To test it, we performed a set of 2D-GE experiments on plasma samples from 9 patients victims of acute myocardial infarction and 8 controls, and we compared the results obtained by our procedure to those obtained using a widely diffuse commercial package, finding similar performance

Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

BACKGROUND: Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. RESULTS: Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. CONCLUSIONS: Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa

A novel method of combining blood oxygenation and blood flow sensitive magnetic resonance imaging techniques to measure the cerebral blood flow and oxygen metabolism responses to an unknown neural stimulus.

Simultaneous implementation of magnetic resonance imaging methods for Arterial Spin Labeling (ASL) and Blood Oxygenation Level Dependent (BOLD) imaging makes it possible to quantitatively measure the changes in cerebral blood flow (CBF) and cerebral oxygen metabolism (CMRO(2)) that occur in response to neural stimuli. To date, however, the range of neural stimuli amenable to quantitative analysis is limited to those that may be presented in a simple block or event related design such that measurements may be repeated and averaged to improve precision. Here we examined the feasibility of using the relationship between cerebral blood flow and the BOLD signal to improve dynamic estimates of blood flow fluctuations as well as to estimate metabolic-hemodynamic coupling under conditions where a stimulus pattern is unknown. We found that by combining the information contained in simultaneously acquired BOLD and ASL signals through a method we term BOLD Constrained Perfusion (BCP) estimation, we could significantly improve the precision of our estimates of the hemodynamic response to a visual stimulus and, under the conditions of a calibrated BOLD experiment, accurately determine the ratio of the oxygen metabolic response to the hemodynamic response. Importantly we were able to accomplish this without utilizing a priori knowledge of the temporal nature of the neural stimulus, suggesting that BOLD Constrained Perfusion estimation may make it feasible to quantitatively study the cerebral metabolic and hemodynamic responses to more natural stimuli that cannot be easily repeated or averaged

Transverse Spin Structure of the Nucleon through Target Single Spin Asymmetry in Semi-Inclusive Deep-Inelastic (e,e′π±)(e,e^\prime \pi^\pm) Reaction at Jefferson Lab

Jefferson Lab (JLab) 12 GeV energy upgrade provides a golden opportunity to perform precision studies of the transverse spin and transverse-momentum-dependent structure in the valence quark region for both the proton and the neutron. In this paper, we focus our discussion on a recently approved experiment on the neutron as an example of the precision studies planned at JLab. The new experiment will perform precision measurements of target Single Spin Asymmetries (SSA) from semi-inclusive electro-production of charged pions from a 40-cm long transversely polarized $^3$He target in Deep-Inelastic-Scattering kinematics using 11 and 8.8 GeV electron beams. This new coincidence experiment in Hall A will employ a newly proposed solenoid spectrometer (SoLID). The large acceptance spectrometer and the high polarized luminosity will provide precise 4-D ($x$, $z$, $P_T$ and $Q^2$) data on the Collins, Sivers, and pretzelocity asymmetries for the neutron through the azimuthal angular dependence. The full 2$\pi$ azimuthal angular coverage in the lab is essential in controlling the systematic uncertainties. The results from this experiment, when combined with the proton Collins asymmetry measurement and the Collins fragmentation function determined from the e$^+$e$^-$ collision data, will allow for a quark flavor separation in order to achieve a determination of the tensor charge of the d quark to a 10% accuracy. The extracted Sivers and pretzelocity asymmetries will provide important information to understand the correlations between the quark orbital angular momentum and the nucleon spin and between the quark spin and nucleon spin.Comment: 23 pages, 13 figures, minor corrections, matches published versio

Spatial audio in small display screen devices

Our work addresses the problem of (visual) clutter in mobile device interfaces. The solution we propose involves the translation of technique-from the graphical to the audio domain-for expliting space in information representation. This article presents an illustrative example in the form of a spatialisedaudio progress bar. In usability tests, participants performed background monitoring tasks significantly more accurately using this spatialised audio (a compared with a conventional visual) progress bar. Moreover, their performance in a simultaneously running, visually demanding foreground task was significantly improved in the eye-free monitoring condition. These results have important implications for the design of multi-tasking interfaces for mobile devices

Improved precision with Hologic Apex software.

UnlabelledThe precision of Hologic Apex v2.0 analysis software is significantly improved from Hologic Delphi v11.2 software and is comparable to GE Lunar Prodigy v7.5 software. Apex and Delphi precisions were, respectively, 1.0% vs. 1.2% (L1-L4 spine), 1.l % vs. 1.3% (total femur), 1.6% vs. 1.9% (femoral neck), and 0.7% vs. 0.9% (dual total femur).IntroductionPrecision of bone mineral density (BMD) measurements by dual-energy X-ray absorptiometry (DXA) is known to vary by manufacturer, model, and technologist. This study evaluated the precision of three analysis versions: Apex v2.0 and Delphi v11.2 (Hologic, Inc.), and Prodigy v7.5 (GE Healthcare, Inc.) independent of technologist skill.MethodsDuplicate spine and dual hip scans on 90 women were acquired on both Delphi and Prodigy DXA systems at three clinics. BMD measures were converted to standardized BMD (sBMD) units. Precision errors were described as a root-mean-square (RMS) standard deviations and RMS percent coefficients of variation across the population.ResultsApex and Delphi values were highly correlated (r ranged from 0.90 to 0.99). Excluding the right neck, the Apex precision error was found to be 20% to 25% lower than the Delphi (spine: 1.0% versus 1.2% (p < 0.05), total hip: 1.1% versus 1.3% (p < 0.05), right neck: 2.3% versus 2.6% (p > 0.1)). No statistically significant differences were found in the precision error of the Apex and Prodigy (p > 0.05) except for the right neck (2.3% versus 1.8% respectively, p = 0.03).ConclusionThe Apex software has significantly lower precision error compared to Delphi software with similar mean values, and similar precision to that of the Prodigy

A distinct sortase SrtB anchors and processes a streptococcal adhesin AbpA with a novel structural property.

Surface display of proteins by sortases in Gram-positive bacteria is crucial for bacterial fitness and virulence. We found a unique gene locus encoding an amylase-binding adhesin AbpA and a sortase B in oral streptococci. AbpA possesses a new distinct C-terminal cell wall sorting signal. We demonstrated that this C-terminal motif is required for anchoring AbpA to cell wall. In vitro and in vivo studies revealed that SrtB has dual functions, anchoring AbpA to the cell wall and processing AbpA into a ladder profile. Solution structure of AbpA determined by NMR reveals a novel structure comprising a small globular α/β domain and an extended coiled-coil heliacal domain. Structural and biochemical studies identified key residues that are crucial for amylase binding. Taken together, our studies document a unique sortase/adhesion substrate system in streptococci adapted to the oral environment rich in salivary amylase

Sediment Assessment of the Barrow Reservoirs

Aim: To assess the sediment depth and character at ten pre-determined locations in the Barrow reservoirs

Orthogonal Range Reporting and Rectangle Stabbing for Fat Rectangles

In this paper we study two geometric data structure problems in the special case when input objects or queries are fat rectangles. We show that in this case a significant improvement compared to the general case can be achieved. We describe data structures that answer two- and three-dimensional orthogonal range reporting queries in the case when the query range is a \emph{fat} rectangle. Our two-dimensional data structure uses $O(n)$ words and supports queries in $O(\log\log U +k)$ time, where $n$ is the number of points in the data structure, $U$ is the size of the universe and $k$ is the number of points in the query range. Our three-dimensional data structure needs $O(n\log^{\varepsilon}U)$ words of space and answers queries in $O(\log \log U + k)$ time. We also consider the rectangle stabbing problem on a set of three-dimensional fat rectangles. Our data structure uses $O(n)$ space and answers stabbing queries in $O(\log U\log\log U +k)$ time.Comment: extended version of a WADS'19 pape

Breakfast Eating Habits among Medical Students

Background: Breakfast is often thought to be the most important meal of the day as it is known to provide energy for the brain and improve learning. It is also known to contribute significantly to the total daily energy and nutrient intake. Skipping breakfast may affect performance during the rest of the day.Aim: To determine the level of breakfast skipping among medical students and its effect on their attention span and level of fatigue during clinical sessions. Design: A descriptive cross-sectional study of breakfast eating habits among medical students at the University of Ghana Medical School, Korle Bu-Accra. Setting: The University of Ghana Medical School, Korle Bu-Accra.Method: Questionnaires were distributed to second year (pre-clinical) medical students studying the basic sciences and clinical students in ophthalmology to be self-administered. Interview data was captured and analyzed using SPSS version 17.0.Results: The total number of pre-clinical students recruited was 154 and clinical students 163 bringing to a total of 317 students made up of 203 males and 114 females (M: F=1.8:1). The overall breakfast skipping among the students was 71.92%. The prevalence among the pre-clinical students was 76.62% and clinical students 67.48%. Generally, breakfast skipping was significantly related to fatigue and poor attention during clinical sessions.Conclusion: This study suggests that the medical students, both pre-clinical and clinical, skip breakfast and this may affect their studies adverselyKeywords: breakfast skipping, medical students, fatigue, attention span, breakfast habit