Automated detection and mapping of electrical activation when electrogram morphology is complex

BackgroundMapping of cardiac electrical activity can be difficult when electrogram morphology is complex. Complex morphology (multiple and changing deflections) causes activation maps to vary when constructed by different analysts, particularly at areas with spatially varying conduction pattern. An algorithm was developed to automatically detect electrogram activation time which is robust to complex morphology.MethodElectrograms, many of which were complex, were collected from 320 canine epicardial border zone sites in five experiments. A library of electrogram activation times were manually marked a priori by two expert analysts. Then an algorithm which combined correlation and error functions was used to compare each input electrogram to library electrogram patterns. The closest match of input to library electrogram was used to estimate activation time. Once activation times at 320 sites were determined, activation maps were automatically constructed on a computerized grid. The algorithm was validated by comparison with activation times determined by the analysts.ResultsThe mean difference between manual and automated marking of activation time in electrograms acquired during reentrant ventricular tachycardia was 2.1 ± 3.9 ms. The mean sensitivity and positive predictive value were 95.9% and 83.8% respectively. The computer-automated marking process was completed within a few seconds and was robust to fractionated electrograms. Measurement error was mostly attributable to 60 Hz noise, which can be rectified with filtering.ConclusionsThe automated algorithm is useful for rapid and accurate automatic marking of multichannel electrograms, some of which may be fractionated, as well as for real-time display of activation maps in clinical electrophysiology or research studies.     

Monitoring communities of small birds: a comparison between mist-netting and counting

Capsule Counting and mist-netting provided different estimates of abundance.

Aims To compare the efficiency, constraint and bias of mist-netting versus line transects for the estimation of species richness and abundance of passerines.

Methods Mist-nets (126 linear metres) placed crossing a 420 m-long hedgerow line, open for four hours starting at dawn, four days per month from June 2006 to May 2007. During this same period, we conducted a transect parallel to a 1.3-km hedgerow line, four times per month.

Results Estimation of species richness did not vary between methods, even when controlling for ecological groups, whereas the abundance estimations did vary.

Conclusions Overall, line transects are better than mist-netting for estimating species richness and abundance since they are less costly, less invasive, and less time-consuming. However, if fine ecological analyses are required, including species abundance, mist-netting is preferred for solitary passerines that feed on insects and forage in the foliage, and line transects are better for gregarious passerines that feed on seeds or forage on the ground.     

Food and foraging behaviour of the Snares fernbird

Abstract

The Snares fernbird (Bowdleria punctata caudata Buller, 1894) is an opportunistic insectivore, its prey ranging greatly in size and type. Birds forage over a wide variety of sites, including forest, tussock, boulder beaches, cliffs, penguin colonies, and floating kelp. Foraging methods vary with the prey sought, and at times birds adopt specific “search images” when hunting certain insects. Details of foods brought to nestlings are given. Four postures used by fernbirds when foraging actively are described.     

Prefeeding larval development time is not correlated with egg size in regular echinoids (Strongylocentrotus species)

Summary

We compared prefeeding development times, from fertilized egg to prism larva, for Strongylocentrotus embryos from four clutches of eggs (each from a different species) differing in size. Development times did not vary consistently with egg diameter, and trends among eggs of different sizes varied with stage of development. In some cases, development times for eggs of intermediate diameter (S. franciscanus) were longer than those for larger or smaller eggs. Although mean egg diameters in clutches ranged from 84 μm (S. purpuratus) to 162 μm (S. pallidus), differences in development time to the last embryonic stage (prism) were very small. We conclude that the inverse relationship between parental investment in offspring and premetamorphic development time in echinoids depends only on the functional consequences of reduced size of feeding larval stages: effects of egg size on prefeeding development time are not evident.     

A model-based high throughput method for fecundity estimation in fruit fly studies

ABSTRACT

The ability to quantify fecundity is critically important to a wide range of experimental applications, particularly in widely-used model organisms such as Drosophila melanogaster. However, the standard method of manually counting eggs is time consuming and limits the feasibility of large-scale experiments. We develop a predictive model to automate the counting of eggs from images of eggs removed from the media surface and washed onto dark filter paper. Our method uses the simple relationship between the white area in an image and the number of eggs present to create a predictive model that performs well even at high egg densities where clumping can complicate the individual identification of eggs. A cross-validation approach demonstrates our method performs well, with a correlation between predicted and manually counted values of 0.88. We show how this method can be applied to a large data set where egg densities vary widely.     

Post-stroke infection: A systematic review and meta-analysis

Background  

stroke is the main cause of disability in high-income countries, and ranks second as a cause of death worldwide. Patients with acute stroke are at risk for infections, but reported post-stroke infection rates vary considerably. We performed a systematic review and meta-analysis to estimate the pooled post-stroke infection rate and its effect on outcome.     

Taro (<Emphasis Type="Italic">Colocasia esculenta</Emphasis> [L.] Schott) Cultivation in Vertical Wet-Dry Environments: Farmers’ Techniques and Cultivar Diversity in Southwestern Ethiopia

Taro (Colocasia esculenta [L.] Schott) Cultivation in Vertical Wet-Dry Environments: Farmers’ Techniques and Cultivar Diversity in Southwestern Ethiopia. Taro (Colocasia esculenta [L.] Schott) is a food crop that was domesticated in Asia and the Pacific region and is now grown in the humid tropics. Following its arrival in Africa in ancient times, it may have adapted to the drier environments. In this ethnographic study, I present a particular case of taro cultivation and uses by a group of farmers in the mountains of southwestern Ethiopia. There are 36 named cultivars of taro for which diversity is maintained through different cultivation techniques and culinary practices in wet and dry environments that vary in elevation. Because taro in dry lowland environments has recently been replaced by the introduction of new crops, it is possible that the drought-tolerant eddoe-type cultivars, which are traditionally dominant in Africa, are now in danger of disappearing.     

Estimating similarity of communities: a parametric approach to spatio‐temporal analysis of species diversity

Several stochastic models with environmental noise generate spatio‐temporal Gaussian fields of log densities for the species in a community. Combinations of such models for many species often lead to lognormal species abundance distributions. In spatio‐temporal analysis it is often realistic to assume that the same species are expected to occur at different times and/or locations because extinctions are rare events. Spatial and temporal β‐diversity can then be analyzed by studying pairs of communities at different times or locations defined by a bivariate lognormal species abundance model in which a single correlation occurs. This correlation, which is a measure of similarity between two communities, can be estimated from samples even if the sampling intensities vary and are unknown, using the bivariate Poisson lognormal distribution. The estimators are approximately unbiased, although each specific correlation may be rather uncertain when the sampling effort is low with only a small fraction of the species represented in the samples. An important characteristic of this community correlation is that it relates to the classical Jaccard‐ or the Sørensen‐indices of similarity based on the number of species present or absent in two communities. However, these indices calculated from samples of species in a community do not necessarily reflect similarity of the communities because the observed number of species depends strongly on the sampling intensities. Thus, we propose that our community correlation should be considered as an alternative to these indices when comparing similarity of communities. We illustrate the application of the correlation method by computing the similarity between temperate bird communities.     

Dynamic Structure of Proteins in Solid State. 1H and 13C NMR Relaxation Study

Abstract

Temperature dependencies of ¹H non-selective NMR T₁ and T₂ relaxation times measured at two resonance frequencies and natural abundance ^l3C NMR relaxation times T_l and T_lr measured at room temperature have been studied in a set of dry and wet solid proteins—;Bacterial RNase, lysozyme and Bovine serum albumin (BSA). The proton and carbon data were interpreted in terms of a model supposing three kinds of internal motions in a protein. These are rotation of the methyl protons around the axis of symmetry of the methyl group, and fast and slow oscillations of all atoms. The correlation times of these motions in solid state are found around 10^?11, 10^?9 and 10^?6 s, respectively. All kinds of motion are characterized by the inhomogeneous distribution of the correlation times. The protein dehydration affects only the slow internal motion. The amplitude of the slow motion obtained from the carbon data is substantially less than that obtained from the proton data. This difference can be explained by taking into account different relative inter- and intra- chemical group contributions to the proton and carbon second moments. The comparison of the solid state and solution proton relaxation data showed that the internal protein dynamics in these states is different: the slow motion seems to be few orders of magnitude faster in solution.     

Effect of Confinement on Melting in Slit-Shaped Pores: Experimental and Simulation Study of Aniline in Activated Carbon Fibers

Abstract

We report both experimental and molecular simulation studies of the melting behavior of aniline confined within an activated carbon fiber having slit-shaped pores. Dielectric relaxation spectroscopy is used to determine the transition temperatures and also the dielectric relaxation times over the temperature range 240 to 340 K. For the confined system two transitions were observed, one at 298 K and a second transition at 324 K. The measured relaxation times indicate that the low temperature phase (below 298 K) is a crystalline or partially crystalline solid phase, while that above 324 K is a liquid-like phase; for the intermediate phase, in the range 298–324 K, the relaxation times are of the order 10^?5s, which is typical of a hexatic phase. The melting temperature of the confined system is well above that of bulk aniline, which is 267 K. The simulations are carried out using the Grand Canonical Monte Carlo method together with Landau free energy calculations, and phase transitions are located as state points where the grand free energies of two confined phases are equal. The nature of these phases is determined by analysis of in-plane pair positional and orientational correlation functions. The simulations also show two transitions. The first is a transition from a two-dimensional hexagonal crystal phase to a hexatic phase at 296 K; the second transition is from the hexatic to a liquid-like phase at 336 K. Confinement within the slit-shaped pores appears to stabilize the hexatic phase, which is the stable phase over a wider temperature range than for quasi-two-dimensional thin films.     

What explains the differences between centres in the European screening trial? A simulation study

BackgroundThe European Randomised study of Screening for Prostate Cancer (ERSPC) is a multicentre, randomised screening trial on men aged 55–69 years at baseline without known prostate cancer (PrCa) at randomisation to an intervention arm invited to screening or to a control arm. The ERSPC has shown a significant 21% reduction in PrCa mortality at 13 years of follow-up. The effect of screening appears to vary across centres, for which several explanations are possible. We set to assess if the apparent differences in PrCa mortality reduction between the centres can be explained by differences in screening protocols.MethodsWe examined the centre differences by developing a simulation model and estimated how alternative screening protocols would have affected PrCa mortality.ResultsOur results showed outcomes similar to those observed, when the results by centres were reproduced by simulating the screening regimens with PSA threshold of 3 versus 4 ng/ml, or screening interval of two versus four years. The findings suggest that the differences are only marginally attributable to the different screening protocols.ConclusionThe small screening impact in Finland was not explained by the differences in the screening protocols. A possible reason for it was the contamination of and the unexpectedly low PrCa mortality in the Finnish control arm.     

Differential Expression of Inflammatory Cytokines and Stress Genes in Male and Female Mice in Response to a Lipopolysaccharide Challenge

BackgroundSex plays a key role in an individual’s immune response against pathogenic challenges such that females fare better when infected with certain pathogens. It is thought that sex hormones impact gene expression in immune cells and lead to sexually dimorphic responses to pathogens. We predicted that, in the presence of E. coli gram-negative lipopolysaccharide (LPS), there would be a sexually dimorphic response in proinflammatory cytokine production and acute phase stress gene expression and that these responses might vary among different mouse strains and times in a pattern opposite to that of body temperature associated with LPS-induced shock.ResultsStatistical analysis using analyses of variance (ANOVAs) showed that the levels of the all six traits changed over time, generally peaking at 2 hours after LPS injection. Mt-1, Fgb, and IL-6 showed differences among strains, although these were time-specific. Sexual dimorphism was seen for Fgb and IL6, and was most pronounced at the latest time period (7 hours) where male levels exceeded those for females. Trends for all six cytokine/gene expression traits were negatively correlated with those for body temperatures.DiscussionThe higher levels of expression of Fgb and IL6 in males compared with females are consistent with the greater vulnerability of males to infection and subsequent inflammation. Temperature appears to be a useful proxy for mortality in endotoxic shock, but sexual dimorphism in cytokine and stress gene expression levels may persist after an LPS challenge even if temperatures in the two sexes are similar and have begun to stabilize.     

The DNA Sequence-dependence of Nucleosome Positioning in vivo and in vitro

Abstract

The contribution of histone-DNA interactions to nucleosome positioning in vivo is currently a matter of debate. We argue here that certain nucleosome positions, often in promoter regions, in yeast may be, at least in part, specified by the DNA sequence. In contrast other positions may be poorly specified. Positioning thus has both statistical and DNA-determined components. We further argue that the relative affinity of the octamer for different DNA sequences can vary and therefore the interaction of histones with the DNA is a ‘tunable’ property.     

Real-time monitoring of non-viable airborne particles correlates with airborne colonies and represents an acceptable surrogate for daily assessment of cell-processing cleanroom performance

Background aimsAirborne particulate monitoring is mandated as a component of good manufacturing practice. We present a procedure developed to monitor and interpret airborne particulates in an International Organization for Standardization (ISO) class 7 cleanroom used for the cell processing of Section 351 and Section 361 products.MethodsWe collected paired viable and non-viable airborne particle data over a period of 1 year in locations chosen to provide a range of air quality. We used receiver operator characteristic (ROC) analysis to determine empirically the relationship between non-viable and viable airborne particle counts.ResultsViable and non-viable particles were well-correlated (r² = 0.78), with outlier observations at the low end of the scale (non-viable particles without detectable airborne colonies). ROC analysis predicted viable counts ≥ 0.5/feet³ (a limit set by the United States Pharmacopeia) at an action limit of ≥ 32 000 particles (≥ 0.5 µ)/feet³, with 95.6% sensitivity and 50% specificity. This limit was exceeded 2.6 times during 18 months of retrospective daily cleanroom data (an expected false alarm rate of 1.3 times/year). After implementing this action limit, we were alerted in real time to an air-handling failure undetected by our hospital facilities management.ConclusionsA rational action limit for non-viable particles was determined based on the correlation with airborne colonies. Reaching or exceeding the action limit of 32 000 non-viable particles/feet³ triggers suspension of cleanroom cell-processing activities, deep cleaning, investigation of air handling, and a deviation management process. Our full procedure for particle monitoring is available as an online supplement.     

Cytoplasmic streaming in internodal cells ofNitella under centrifugal acceleration: a study done with a newly constructed centrifuge microscope

Summary We constructed a new centrifuge microscope of the stroboscopic type, with which the cytoplasmic streaming inNitella internodal cells under centrifugal acceleration was studied. Under moderate centrifugal acceleration (ca. 50–100×g), the direction of cytoplasmic streaming in an internodal cell ofNitella is parallel to the direction of the subcortical fibrils. The speed of endoplasm flowing contiguous to the subcortical fibrils is neither accelerated nor retarded by moderate centrifugal acceleration. The endoplasmic flow, however, stops suddenly following an electrical stimulus. The endoplasm contiguous to the subcortical fibrils is immobilized transiently at the time of streaming cessation induced by an electrical stimulus under centrifugal acceleration at 50–100×g, even at 900×g. It is suggested that transitory cross bridges between the immobilized endoplasm and the subcortical fibrils are formed at the time of streaming cessation. The bulk endoplasm flows as a whole in the direction parallel to that of the subcortical fibrils and stops promptly upon electrical stimulation. Soon after the stoppage the bulk endoplasm starts to flow passively in the direction parallel to that of the centrifugal acceleration as a result of the centrifugal force.Abbreviations APW artificial pond water - CMS centrifuge microscope     

Light stalks increase the precision and accuracy of non-breeding locations calculated from geolocator tags: a field test from a long-distance migrant

ABSTRACT

Capsule: There is a substantial gain in precision and accuracy of geolocator locations when using a light stalk.

Aims: Light stalks or tubes increase the accuracy of geolocators when tracking migrant birds because they reduce potential shading of the light sensor by feathers but may increase detrimental tag effects. We aimed to determine how adding light stalks to geolocator tags increased accuracy and precision of locations.

Methods: We quantified how precision and accuracy of geolocator locations was affected by comparing variation of sunrise and sunset times from tags with variable length light stalks (6 of 0?mm, 8 of 5?mm and 21 of 10?mm). Tags were fitted to Whinchats Saxicola rubetra in central Nigeria (the known location to compare accuracy), and variance in latitude and longitude of geolocator estimated locations were also compared across light stalk lengths during spring migration stationary locations, and at breeding sites in Eastern Europe, for both Geolight and FlightR methods.

Results: Without a light stalk, the standard deviation of sunset and sunrise times increased by 50% and 100%, respectively (i.e. less precise): confidence intervals for latitude were larger by about 4.3 degrees at non-breeding low latitudes and 1.8 degrees at stop-over latitudes, or confidence intervals for longitude were larger by 2.3 degrees, dependent on analysis method. Estimated sun elevation angles were significantly less accurate and so calculated non-breeding locations were significantly less accurate by about 8 degrees of latitude. Precision in sunrise, sunset times, latitude and longitude, was similar when using a 5?mm or 10?mm stalk.

Conclusions: The results show a substantial gain in precision and accuracy of low latitude geolocator locations when using a light stalk that brings the sensor above covering feathers. There is no advantage from longer light stalk lengths than those necessary to just expose the light sensor above the feathers, at least for small passerines.     

Chimeras Reveal a Single Lipid-Interface Residue that Controls MscL Channel Kinetics as well as Mechanosensitivity

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Highlights? MscL from E. coli and S. aureus are functionally distinct mechanosensitive channels ? MscL chimeras allow correlation of structural differences with functional variance ? Residue hydropathy at one site influences gating and state stabilization of MscL ? One residue can vary MscL activity similarly to adjusting a spring of a clasp knife     

The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability

Background and AimsPlant genomes contain many retrotransposons and their derivatives, which are subject to rapid sequence turnover. As non-autonomous retrotransposons do not encode any proteins, they experience reduced selective constraints leading to their diversification into multiple families, usually limited to a few closely related species. In contrast, the non-coding Cassandra terminal repeat retrotransposons in miniature (TRIMs) are widespread in many plants. Their hallmark is a conserved 5S rDNA-derived promoter in their long terminal repeats (LTRs). As sugar beet (Beta vulgaris) has a well-described LTR retrotransposon landscape, we aim to characterize TRIMs in beet and related genomes.MethodsWe identified Cassandra retrotransposons in the sugar beet reference genome and characterized their structural relationships. Genomic organization, chromosomal localization, and distribution of Cassandra-TRIMs across the Amaranthaceae were verified by Southern and fluorescent in situ hybridization.Key resultsAll 638 Cassandra sequences in the sugar beet genome contain conserved LTRs and thus constitute a single family. Nevertheless, variable internal regions required a subdivision into two Cassandra subfamilies within B. vulgaris. The related Chenopodium quinoa harbours a third subfamily. These subfamilies vary in their distribution within Amaranthaceae genomes, their insertion times and the degree of silencing by small RNAs. Cassandra retrotransposons gave rise to many structural variants, such as solo LTRs or tandemly arranged Cassandra retrotransposons. These Cassandra derivatives point to an interplay of template switch and recombination processes – mechanisms that likely caused Cassandra’s subfamily formation and diversification.ConclusionsWe traced the evolution of Cassandra in the Amaranthaceae and detected a considerable variability within the short internal regions, whereas the LTRs are strongly conserved in sequence and length. Presumably these hallmarks make Cassandra a prime target for unequal recombination, resulting in the observed structural diversity, an example of the impact of LTR-mediated evolutionary mechanisms on the host genome.     

Biochemical investigations of the nuclear proteins during the transition of root meristems from quiescent to proliferating state in Pisum sativum

Abstract

The electrophoretic analysis of nuclear proteins extracted from root meristems at different times of germination puts in evidence the variations of content of specific proteins. Several nuclear proteins are phosphorylated by endogenous protein kinase and often the maximum rate of phosphorylation it has been observed in proteins present in the nucleus at low concentrations. Moreover also the phosphorylation rate of specific proteins changes at different times of germination. It is interesting the fact that both variations of concentration and phosphorylation in nuclear proteins occurr at the time when root meristems leave the quiescence to enter a proliferating state. We suggest that these variations play a role in this physiological event.