Autopiquer - a robust and reliable peak detection algorithm for mass spectrometry

We present a simple algorithm for robust and unsupervised peak detection by determining a noise threshold in isotopically resolved mass spectrometry data. Solving this problem will greatly reduce the subjective and time consuming manual picking of mass spectral peaks and so will prove beneficial in many research applications. The Autopiquer approach uses autocorrelation to test for the presence of (isotopic) structure in overlapping windows across the spectrum. Within each window, a noise threshold is optimized to remove the most unstructured data whilst keeping as much of the (isotopic) structure as possible. This algorithm has been successfully demonstrated for both peak detection and spectral compression on data from many different classes of mass spectrometer and for different sample types and this approach should also be extendible to other types of data that contain regularly spaced discrete peaks

End-User Development of Voice User Interfaces based on Web content

Voice Assistants, and particularly the latest gadgets called smart speakers, allow end users to interact with applications by means of voice commands. As usual, end users are able to install applications (also called skills) that are available in repositories and fulfill multiple purposes. In this work we present an end-user environment to define skills for voice assistants based on the extraction of Web content and their organization into different voice navigation patterns. We describe the approach, the end-user development environment, and finally we present some case studies based on Alexa and Amazon Echo

Inactivation of Poxviruses by Upper-Room UVC Light in a Simulated Hospital Room Environment

In the event of a smallpox outbreak due to bioterrorism, delays in vaccination programs may lead to significant secondary transmission. In the early phases of such an outbreak, transmission of smallpox will take place especially in locations where infected persons may congregate, such as hospital emergency rooms. Air disinfection using upper-room 254 nm (UVC) light can lower the airborne concentrations of infective viruses in the lower part of the room, and thereby control the spread of airborne infections among room occupants without exposing occupants to a significant amount of UVC. Using vaccinia virus aerosols as a surrogate for smallpox we report on the effectiveness of air disinfection, via upper-room UVC light, under simulated real world conditions including the effects of convection, mechanical mixing, temperature and relative humidity. In decay experiments, upper-room UVC fixtures used with mixing by a conventional ceiling fan produced decreases in airborne virus concentrations that would require additional ventilation of more than 87 air changes per hour. Under steady state conditions the effective air changes per hour associated with upper-room UVC ranged from 18 to 1000. The surprisingly high end of the observed range resulted from the extreme susceptibility of vaccinia virus to UVC at low relative humidity and use of 4 UVC fixtures in a small room with efficient air mixing. Increasing the number of UVC fixtures or mechanical ventilation rates resulted in greater fractional reduction in virus aerosol and UVC effectiveness was higher in winter compared to summer for each scenario tested. These data demonstrate that upper-room UVC has the potential to greatly reduce exposure to susceptible viral aerosols. The greater survival at baseline and greater UVC susceptibility of vaccinia under winter conditions suggest that while risk from an aerosol attack with smallpox would be greatest in winter, protective measures using UVC may also be most efficient at this time. These data may also be relevant to influenza, which also has improved aerosol survival at low RH and somewhat similar sensitivity to UVC

The MC1R gene in the guppy (Poecilia reticulata): Genotypic and phenotypic polymorphisms

<p>Abstract</p> <p>Background</p> <p>The guppy (<it>Poecilia reticulata</it>) is an important model organism for studying sexual selection; male guppies have complex and conspicuous pigmentation, and female guppies exhibit preferences for males with specific color spots. Understanding the genetic basis underlying pigmentation variation in the guppy is important for exploring the factors causing the maintenance of color polymorphism in wild populations.</p> <p>Findings</p> <p>We focused on the melanic black pigmentation of guppies, and examined genetic variations in the <it>melanocortin 1 receptor </it>(<it>MC1R</it>) gene because variation in this gene is known to contribute to polymorphism of melanin pigmentation in several animal species. The complete coding sequence of the guppy <it>MC1R </it>gene was determined, and two different <it>MC1R </it>alleles (963 and 969 bp) were found in wild populations. Ornamental strain guppies with a 963-bp <it>MC1R </it>tended to show less black pigmentation than those with a 969-bp <it>MC1R</it>, although the association between <it>MC1R </it>genotype and black pigmentation disappeared in the F₂offspring.</p> <p>Conclusions</p> <p>The guppy <it>MC1R </it>gene showed variation in the five wild Trinidadian populations we examined, and these populations also differed in terms of allele frequencies. We identified a significant association between black pigmentation and <it>MC1R </it>genotype in fish obtained from aquarium shops. However, the results from F₂families suggest that there are other genes that modify the effects of the <it>MC1R </it>gene.</p

Human bipedal instability in tree canopy environments is reduced by “light touch” fingertip support

Whether tree canopy habitats played a sustained role in the ecology of ancestral bipedal hominins is unresolved. Some argue that arboreal bipedalism was prohibitively risky for hominins whose increasingly modern anatomy prevented them from gripping branches with their feet. Balancing on two legs is indeed challenging for humans under optimal conditions let alone in forest canopy, which is physically and visually highly dynamic. Here we quantify the impact of forest canopy characteristics on postural stability in humans. Viewing a movie of swaying branches while standing on a branch-like bouncy springboard destabilised the participants as much as wearing a blindfold. However “light touch”, a sensorimotor feedback strategy based on light fingertip support, significantly enhanced their balance and lowered their thigh muscle activity by up to 30%. This demonstrates how a light touch strategy could have been central to our ancestor’s ability to avoid falls and reduce the mechanical and metabolic cost of arboreal feeding and movement. Our results may also indicate that some adaptations in the hand that facilitated continued access to forest canopy may have complemented, rather than opposed, adaptations that facilitated precise manipulation and tool use

Reproducibility of 3-dimensional ultrasound readings of volume of carotid atherosclerotic plaque

<p>Abstract</p> <p>Background</p> <p>Non-invasive 3-dimensional (3D) ultrasound (US) has emerged as the predominant approach for evaluating the progression of carotid atherosclerosis and its response to treatment. The aim of this study was to investigate the quality of a central reading procedure concerning plaque volume (PV), measured by 3D US in a multinational US trial.</p> <p>Methods</p> <p>Two data sets of 45 and 60 3D US patient images of plaques (mean PV, 71.8 and 39.8 μl, respectively) were used. PV was assessed by means of manual planimetry. The intraclass correlation coefficient (ICC) was applied to determine reader variabilities. The repeatability coefficient (RC) and the coefficient of variation (CV) were used to investigate the effect of number of slices (S) in manual planimetry and plaque size on measurement variability.</p> <p>Results</p> <p>Intra-reader variability was small as reflected by ICCs of 0.985, 0.967 and 0.969 for 3 appointed readers. The ICC value generated between the 3 readers was 0.964, indicating that inter-reader variability was small, too. Subgroup analyses showed that both intra- and inter-reader variabilities were lower for larger than for smaller plaques. Mean CVs were similar for the 5S- and 10S-methods with a RC of 4.7 μl. The RC between both methods as well as the CVs were comparatively lower for larger plaques.</p> <p>Conclusion</p> <p>By implementing standardised central 3D US reading protocols and strict quality control procedures highly reliable ultrasonic re-readings of plaque images can be achieved in large multicentre trials.</p

Constitutive Activation of the Thyroid-Stimulating Hormone Receptor (TSHR) by Mutating Ile691 in the Cytoplasmic Tail Segment

/inositol phosphate (IP) pathways, which stimulate thyroid hormone production and thyroid proliferation./IP signaling pathway./IP cascade