The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa

BACKGROUND: Chorismate mutases of the AroQ homology class are widespread in the Bacteria and the Archaea. Many of these exist as domains that are fused with other aromatic-pathway catalytic domains. Among the monofunctional AroQ proteins, that from Erwinia herbicola was previously shown to have a cleavable signal peptide and located in the periplasmic compartment. Whether or not this might be unique to E. herbicola was unknown. RESULTS: The gene coding for the AroQ protein was cloned from Salmonella typhimurium, and the AroQ protein purified from both S. typhimurium and Pseudomonas aeruginosa was shown to have a periplasmic location. The periplasmic chorismate mutases (denoted *AroQ) are shown to be a distinct subclass of AroQ, being about twice the size of cytoplasmic AroQ proteins. The increased size is due to a carboxy-terminal extension of unknown function. In addition, a so-far novel aromatic aminotransferase was shown to be present in the periplasm of P. aeruginosa. CONCLUSIONS: Our analysis has detected a number of additional *aroQ genes. The joint presence of *AroQ, cyclohexadienyl dehydratase and aromatic aminotransferase in the periplasmic compartment of P. aeruginosa comprises a complete chorismate-to-phenylalanine pathway and accounts for the "hidden overflow pathway" to phenylalanine described previously

Seal whiskers vibrate over broad frequencies during hydrodynamic tracking

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 8350, doi:10.1038/s41598-017-07676-w.Although it is known that seals can use their whiskers (vibrissae) to extract relevant information from complex underwater flow fields, the underlying functioning of the system and the signals received by the sensors are poorly understood. Here we show that the vibrations of seal whiskers may provide information about hydrodynamic events and enable the sophisticated wake-tracking abilities of these animals. We developed a miniature accelerometer tag to study seal whisker movement in situ. We tested the ability of the tag to measure vibration in excised whiskers in a flume in response to laminar flow and disturbed flow. We then trained a seal to wear the tag and follow an underwater hydrodynamic trail to measure the whisker signals available to the seal. The results showed that whiskers vibrated at frequencies of 100–300 Hz, with a dynamic response. These measurements are the first to capture the incoming signals received by the vibrissae of a live seal and show that there are prominent signals at frequencies where the seal tactogram shows good sensitivity. Tapping into the mechanoreceptive interface between the animal and the environment may help to decipher the functional basis of this extraordinary hydrodynamic detection ability.Funding was provided by the NSF GRFP and NISE section 219 to C. Murphy and by the Office of Naval Research (N000141910468) to B. Calhoun

Whole MILC: generalizing learned dynamics across tasks, datasets, and populations

Behavioral changes are the earliest signs of a mental disorder, but arguably, the dynamics of brain function gets affected even earlier. Subsequently, spatio-temporal structure of disorder-specific dynamics is crucial for early diagnosis and understanding the disorder mechanism. A common way of learning discriminatory features relies on training a classifier and evaluating feature importance. Classical classifiers, based on handcrafted features are quite powerful, but suffer the curse of dimensionality when applied to large input dimensions of spatio-temporal data. Deep learning algorithms could handle the problem and a model introspection could highlight discriminatory spatio-temporal regions but need way more samples to train. In this paper we present a novel self supervised training schema which reinforces whole sequence mutual information local to context (whole MILC). We pre-train the whole MILC model on unlabeled and unrelated healthy control data. We test our model on three different disorders (i) Schizophrenia (ii) Autism and (iii) Alzheimers and four different studies. Our algorithm outperforms existing self-supervised pre-training methods and provides competitive classification results to classical machine learning algorithms. Importantly, whole MILC enables attribution of subject diagnosis to specific spatio-temporal regions in the fMRI signal.Comment: Accepted at MICCAI 2020. arXiv admin note: substantial text overlap with arXiv:1912.0313

An ICA with reference approach in identification of genetic variation and associated brain networks

To address the statistical challenges associated with genome-wide association studies, we present an independent component analysis (ICA) with reference approach to target a specific genetic variation and associated brain networks. First, a small set of single nucleotide polymorphisms (SNPs) are empirically chosen to reflect a feature of interest and these SNPs are used as a reference when applying ICA to a full genomic SNP array. After extracting the genetic component maximally representing the characteristics of the reference, we test its association with brain networks in functional magnetic resonance imaging (fMRI) data. The method was evaluated on both real and simulated datasets. Simulation demonstrates that ICA with reference can extract a specific genetic factor, even when the variance accounted for by such a factor is so small that a regular ICA fails. Our real data application from 48 schizophrenia patients (SZs) and 40 healthy controls (HCs) include 300K SNPs and fMRI images in an auditory oddball task. Using SNPs with allelic frequency difference in two groups as a reference, we extracted a genetic component that maximally differentiates patients from controls (p < 4 × 10−17), and discovered a brain functional network that was significantly associated with this genetic component (p < 1 × 10−4). The regions in the functional network mainly locate in the thalamus, anterior and posterior cingulate gyri. The contributing SNPs in the genetic factor mainly fall into two clusters centered at chromosome 7q21 and chromosome 5q35. The findings from the schizophrenia application are in concordance with previous knowledge about brain regions and gene function. All together, the results suggest that the ICA with reference can be particularly useful to explore the whole genome to find a specific factor of interest and further study its effect on brain

Improving the power-delay performance in subthreshold source-coupled logic circuits

Subthreshold source-coupled logic (STSCL) circuits can be used in design of low-voltage and ultra-low power digital systems. This article introduces and analyzes new techniques for implementing complex digital systems using STSCL gates with an improved power-delay product (PDP) based on source-follower output stages. A test chip has been manufactured in a conventional digital 0.18$\mu$m CMOS technology to evaluate the performance of the proposed STSCL circuit, and speed and PDP improvements by a factor of up to 2.4 were demonstrated

The concept of solidarity: emerging from the theoretical shadows?

The concept of solidarity has been relatively neglected by social scientists since Durkheim's pioneering work in the late 19th century. The discipline of politics has been guilty of overlooking this 'subjective' element of community life, but recent works by Stjernø and Brunkhorst reflect a growing awareness of the theoretical significance of the concept. Whereas early liberal attempts to theorise solidarity took the nation state to be the appropriate community for its realisation, the emergence of globalisation raises the possibility of human solidarity developing in the global community. Traditional forms of solidarity have been dissipated by the social changes accompanying globalisation, but they were often locked into the defence of particular interests. New forms may be emerging to rekindle the broader vision of human solidarity. Recent work by writers such as Habermas, Honneth, Rorty and Touraine focuses on widening and deepening democratic participation and/or the articulation of our ethical obligations in various ways. It is argued here that these perspectives need to be supplemented by a radical humanist approach grounded in a normative theory of human self-realisation

Joint Elastic Side-Scattering Lidar and Raman Lidar Measurements of Aerosol Optical Properties in South East Colorado

We describe an experiment, located in south-east Colorado, USA, that measured aerosol optical depth profiles using two Lidar techniques. Two independent detectors measured scattered light from a vertical UV laser beam. One detector, located at the laser site, measured light via the inelastic Raman backscattering process. This is a common method used in atmospheric science for measuring aerosol optical depth profiles. The other detector, located approximately 40km distant, viewed the laser beam from the side. This detector featured a 3.5m2 mirror and measured elastically scattered light in a bistatic Lidar configuration following the method used at the Pierre Auger cosmic ray observatory. The goal of this experiment was to assess and improve methods to measure atmospheric clarity, specifically aerosol optical depth profiles, for cosmic ray UV fluorescence detectors that use the atmosphere as a giant calorimeter. The experiment collected data from September 2010 to July 2011 under varying conditions of aerosol loading. We describe the instruments and techniques and compare the aerosol optical depth profiles measured by the Raman and bistatic Lidar detectors.Comment: 34 pages, 16 figure

Actors and networks or agents and structures: towards a realist view of information systems

Actor-network theory (ANT) has achieved a measure of popularity in the analysis of information systems. This paper looks at ANT from the perspective of the social realism of Margaret Archer. It argues that the main issue with ANT from a realist perspective is its adoption of a `flat' ontology, particularly with regard to human beings. It explores the value of incorporating concepts from ANT into a social realist approach, but argues that the latter offers a more productive way of approaching information systems

High-resolution microwave frequency dissemination on an 86-km urban optical link

We report the first demonstration of a long-distance ultra stable frequency dissemination in the microwave range. A 9.15 GHz signal is transferred through a 86-km urban optical link with a fractional frequency stability of 1.3x10-15 at 1 s integration time and below 10-18 at one day. The optical link phase noise compensation is performed with a round-trip method. To achieve such a result we implement light polarisation scrambling and dispersion compensation. This link outperforms all the previous radiofrequency links and compares well with recently demonstrated full optical links.Comment: 11 pages, 5 figure

Mars Tumbleweed: FY2003 Conceptual Design Assessment

NASA LaRC is studying concepts for a new type of Mars exploration vehicle that would be propelled by the wind. Known as the Mars Tumbleweed, it would derive mobility through use of the Martian surface winds. Tumbleweeds could conceivably travel greater distances, cover larger areas of the surface, and provide access to areas inaccessible by conventional vehicles. They would be lightweight and relatively inexpensive, allowing a multiple vehicle network to be deployed on a single mission. Tumbleweeds would be equipped with sensors for conducting science and serve as scouts searching broad areas to identify specific locations for follow-on investigation by other explorers. An extensive assessment of LaRC Tumbleweed concepts was conducted in FY03, including refinement of science mission scenarios, definition of supporting subsystems (structures, power, communications), testing in wind tunnels, and development of a dynamic simulation capability