Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli

The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H2 during fermentation, its reversibility, allowing H2-dependent CO2 reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex

Statistical relational learning with soft quantifiers

Quantification in statistical relational learning (SRL) is either existential or universal, however humans might be more inclined to express knowledge using soft quantifiers, such as ``most'' and ``a few''. In this paper, we define the syntax and semantics of PSL^Q, a new SRL framework that supports reasoning with soft quantifiers, and present its most probable explanation (MPE) inference algorithm. To the best of our knowledge, PSL^Q is the first SRL framework that combines soft quantifiers with first-order logic rules for modelling uncertain relational data. Our experimental results for link prediction in social trust networks demonstrate that the use of soft quantifiers not only allows for a natural and intuitive formulation of domain knowledge, but also improves the accuracy of inferred results

Distributed Representations of Signed Networks

Recent successes in word embedding and document embedding have motivated researchers to explore similar representations for networks and to use such representations for tasks such as edge prediction, node label prediction, and community detection. Such network embedding methods are largely focused on finding distributed representations for unsigned networks and are unable to discover embeddings that respect polarities inherent in edges. We propose SIGNet, a fast scalable embedding method suitable for signed networks. Our proposed objective function aims to carefully model the social structure implicit in signed networks by reinforcing the principles of social balance theory. Our method builds upon the traditional word2vec family of embedding approaches and adds a new targeted node sampling strategy to maintain structural balance in higher-order neighborhoods. We demonstrate the superiority of SIGNet over state-of-the-art methods proposed for both signed and unsigned networks on several real world datasets from different domains. In particular, SIGNet offers an approach to generate a richer vocabulary of features of signed networks to support representation and reasoning.Comment: Published in PAKDD 201

Integrated stratigraphy of the Waitakian-Otaian Stage boundary stratotype, Early Miocene, New Zealand

The base of the type section of the Otaian Stage at Bluecliffs, South Canterbury, is recognised as the stratotype for the boundary between the Waitakian and Otaian Stages. Principal problems with the boundary are the restriction of existing bioevent proxies to shelf and upper slope environments and its uncertain age. These topics are addressed by a multidisplinary study of a 125 m section about the boundary, which examines its lithostratigraphy, depositional setting, biostratigraphy, correlation, and geochronology. The lower siltstone lithofacies (0-38.5 m) was deposited at upper bathyal depths (200-600 m) in a marginal basin which was partially sheltered from fully oceanic circulation by a submarine high and islands. The site was covered by cool-temperate water and was probably adjacent to the Subtropical Convergence. This unit is succeeded by the banded lithofacies (38.5-106 m) and the upper siltstone lithofacies (basal 19 m studied). Paleodepth probably declined up-sequence, but deposition at shelf depths is not definitely indicated. A cyclic pattern of abundance spikes in benthic and planktonic foraminifera commences 9 m above base and extends to 73 m in the banded lithofacies. Oxygen isotope excursions (up to 2.08%) in Euuvigerina miozea and Cibicides novozelandicus are greatest within the interval containing the abundance spikes. The stage boundary occurs in the banded lithofacies at the highest abundance spike (73 m). Although condensed intervals might affect the completeness of the section, they are not associated with sedimentary discontinuities, and we consider that the section is suitable as a biostratigraphic reference. Spores, pollens, dinoflagellates, calcareous nannofossils, foraminifera, bryozoans, and ostracods are preserved near the boundary, but molluscs principally occur higher, in the shallower upper siltstone lithofacies. Siliceous microfossils are rare. There is considerable scope for further biostratigraphic research. The primary event marking the boundary at 73 m is the appearance of the benthic foraminifer Ehrenbergina marwicki. This is a distinctive and widely distributed event but is restricted to shelf and upper bathyal environments. Supplementary events in planktonic foraminifera and calcareous nannofossils were researched. Highest occurrences of Globigerina brazieri and G. euapertura are recorded at 47 and 58 m. There is a marked decline in relative abundance of Paragloborotalia spp. at 62 m. Helicosphaera carteri becomes more abundant than H. euphratis between 56 and 87 m. These events are not exact proxies for the boundary but they may usefully indicate proximity to it. They occur in the interval of prominent spikes in foraminiferal abundance. The Waitakian-Otaian boundary is dated at 21.7 Ma by strontium isotopes. Stable primary remanence could not be determined in a pilot paleomagnetic study of Bluecliffs specimens. However, specimens trended towards reversed polarity, and remagnetisation great circle analysis will allow directions to be calculated in future collections

Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris

The climate-active gas methane is generated both by biological processes and by thermogenic decomposition of fossil organic material, which forms methane and short-chain alkanes, principally ethane, propane and butane1, 2. In addition to natural sources, environments are exposed to anthropogenic inputs of all these gases from oil and gas extraction and distribution. The gases provide carbon and/or energy for a diverse range of microorganisms that can metabolize them in both anoxic3 and oxic zones. Aerobic methanotrophs, which can assimilate methane, have been considered to be entirely distinct from utilizers of short-chain alkanes, and studies of environments exposed to mixtures of methane and multi-carbon alkanes have assumed that disparate groups of microorganisms are responsible for the metabolism of these gases. Here we describe the mechanism by which a single bacterial strain, Methylocella silvestris, can use methane or propane as a carbon and energy source, documenting a methanotroph that can utilize a short-chain alkane as an alternative to methane. Furthermore, during growth on a mixture of these gases, efficient consumption of both gases occurred at the same time. Two soluble di-iron centre monooxygenase (SDIMO) gene clusters were identified and were found to be differentially expressed during bacterial growth on these gases, although both were required for efficient propane utilization. This report of a methanotroph expressing an additional SDIMO that seems to be uniquely involved in short-chain alkane metabolism suggests that such metabolic flexibility may be important in many environments where methane and short-chain alkanes co-occur

Processing and Characterization of PETI Composites Fabricated by High Temperature VARTM

The use of composites as primary structures on aerospace vehicles has increased dramatically over the past decade. As these advanced structures increase in size and complexity, their production costs have grown significantly. A major contributor to these manufacturing costs is the requirement of elevated processing pressures, during the thermal cure, to create fully consolidated composites. For certain composite parts, high temperature vacuum assisted resin transfer molding (HT-VARTM) can offer reduced fabrication costs compared to conventional autoclave techniques. The process has been successfully used with phenylethynyl terminated imide (PETI) resins developed by NASA LaRC. In the current study, two PETI resins, LARC(TradeMark) PETI-330 and LARC(TradeMark) PETI-8 have been used to make test specimens using HT-VARTM. Based on previous work at NASA LaRC, larger panels with a quasi-isotropic lay-up were fabricated. The resultant composite specimens exhibited void contents <3% by volume depending on the type of carbon fabric preform used. Mechanical properties of the panels were determined at both room and elevated temperatures. These included open-hole compressive (OHC) and short beam shear (SBS) properties. Limited process modeling efforts were carried out including infusion times, composite panel size limitations and fabric permeability characterization. Work has also been carried out to develop new PETI based resins specifically geared towards HT-VARTM. The results of this work are presented herein

Predicting language diversity with complex network

Evolution and propagation of the world's languages is a complex phenomenon, driven, to a large extent, by social interactions. Multilingual society can be seen as a system of interacting agents, where the interaction leads to a modification of the language spoken by the individuals. Two people can reach the state of full linguistic compatibility due to the positive interactions, like transfer of loanwords. But, on the other hand, if they speak entirely different languages, they will separate from each other. These simple observations make the network science the most suitable framework to describe and analyze dynamics of language change. Although many mechanisms have been explained, we lack a qualitative description of the scaling behavior for different sizes of a population. Here we address the issue of the language diversity in societies of different sizes, and we show that local interactions are crucial to capture characteristics of the empirical data. We propose a model of social interactions, extending the idea from, that explains the growth of the language diversity with the size of a population of country or society. We argue that high clustering and network disintegration are the most important characteristics of models properly describing empirical data. Furthermore, we cancel the contradiction between previous models and the Solomon Islands case. Our results demonstrate the importance of the topology of the network, and the rewiring mechanism in the process of language change

THREE-DIMENSIONAL ANALYSIS OF TURBINE ROTOR FLOW INCLUDING TIP CLEARANCE

A 3D Navier-Stokes investigation of a high pressure turbine rotor blade including tip clearance effects is presented. The 3D Navier-Stokes code developed at ONERA solves the three-dimensional unsteady set of mass-averaged Navier-Stokes equations by the finite volume technique. A one step Lax-Wendroff type scheme is used in a rotating frame of reference. An implicit residual smoothing technique has been implemented, which accelerates the convergence towards the steady state. A mixing length model adapted to 3D configurations is used. The turbine rotor flow is calculated at transonic operating conditions. The tip clearance effect is taken into account. The gap region is discretized using more than 55,000 points within a multi-domain approach. The solution accounts for the relative motion of the blade and casing surfaces. The total mesh is composed of five sub-domains and counts 710,000 discretization points

Interpreting and acting upon home blood pressure readings: A qualitative study

This article is made available through the Brunel Open Access Publishing Fund. Copyright @ 2013 Vasileiou et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Recent guidelines recognize the importance of home blood pressure monitoring (HBPM) as an adjunct to clinical measurements. We explored how people who have purchased and use a home blood pressure (BP) monitor make sense of, and act upon, readings and how they communicate with their doctor about the practice of home monitoring. Methods: A qualitative study was designed and participants were purposively recruited from several areas in England, UK. Semi-structured in-depth interviews were conducted with 18 users of home BP monitors. The transcribed data were thematically analysed. Results: Interpretation of home BP readings is complex, and is often characterised by uncertainty. People seek to assess value normality using ‘rules of thumb’, and often aim to identify the potential causes of the readings. This is done by drawing on lay models of BP function and by contextualising the readings to personal circumstances. Based on the perceived causes of the problematic readings, actions are initiated, mostly relating to changes in daily routines. Contacting the doctor was more likely when the problematic readings persisted and could not be easily explained, or when participants did not succeed in regulating their BP through their other interventions. Most users had notified their doctor of the practice of home monitoring, but medical involvement varied, with some participants reporting disinterest or reservations by doctors. Conclusions: Involvement from doctors can help people overcome difficulties and resolve uncertainties around the interpretation of home readings, and ensure that the rules of thumb are appropriate. Home monitoring can be used to strengthen the patient-clinician relationship