Chalmers University of Technology

Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

A scheme within density functional theory is proposed that provides a practical way to generalize to unrestricted geometries the method applied with some success to layered geometries [Phys. Rev. Lett. 91, 126402 (2003)]]. It includes van der Waals forces in a seamless fashion. By expansion to second order in a carefully chosen quantity contained in the long-range part of the correlation functional, the nonlocal correlations are expressed in terms of a density-density interaction formula. It contains a relatively simple parametrized kernel, with parameters determined by the local density and its gradient. The proposed functional is applied to rare gas and benzene dimers, where it is shown to give a realistic description.

Simulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.

The quintessential goal of sensor array signal processing is the estimation of parameters by fusing temporal and spatial information, captured via sampling a wavefield with a set of judiciously placed antenna sensors. The wavefield is assumed to be generated by a finite number of emitters, and contains information about signal parameters characterizing the emitters. A review of the area of array processing is given. The focus is on parameter estimation methods, and many relevant problems are only briefly mentioned. We emphasize the relatively more recent subspace-based methods in relation to beamforming. The article consists of background material and of the basic problem formulation. Then we introduce spectral-based algorithmic solutions to the signal parameter estimation problem. We contrast these suboptimal solutions to parametric methods. Techniques derived from maximum likelihood principles as well as geometric arguments are covered. Later, a number of more specialized research topics are briefly reviewed. Then, we look at a number of real-world problems for which sensor array processing methods have been applied. We also include an example with real experimental data involving closely spaced emitters and highly correlated signals, as well as a manufacturing application example.

Developing a mechanistic understanding of the impact of food structure and composition on human health has increasingly involved simulating digestion in the upper gastrointestinal tract. These simulations have used a wide range of different conditions that often have very little physiological relevance, and this impedes the meaningful comparison of results. The standardized protocol presented here is based on an international consensus developed by the COST INFOGEST network. The method is designed to be used with standard laboratory equipment and requires limited experience to encourage a wide range of researchers to adopt it. It is a static digestion method that uses constant ratios of meal to digestive fluids and a constant pH for each step of digestion. This makes the method simple to use but not suitable for simulating digestion kinetics. Using this method, food samples are subjected to sequential oral, gastric and intestinal digestion while parameters such as electrolytes, enzymes, bile, dilution, pH and time of digestion are based on available physiological data. This amended and improved digestion method (INFOGEST 2.0) avoids challenges associated with the original method, such as the inclusion of the oral phase and the use of gastric lipase. The method can be used to assess the endpoints resulting from digestion of foods by analyzing the digestion products (e.g., peptides/amino acids, fatty acids, simple sugars) and evaluating the release of micronutrients from the food matrix. The whole protocol can be completed in ~7 d, including ~5 d required for the determination of enzyme activities.

Abstract. Secondary organic aerosol (SOA) accounts for a significant fraction of ambient tropospheric aerosol and a detailed knowledge of the formation, properties and transformation of SOA is therefore required to evaluate its impact on atmospheric processes, climate and human health. The chemical and physical processes associated with SOA formation are complex and varied, and, despite considerable progress in recent years, a quantitative and predictive understanding of SOA formation does not exist and therefore represents a major research challenge in atmospheric science. This review begins with an update on the current state of knowledge on the global SOA budget and is followed by an overview of the atmospheric degradation mechanisms for SOA precursors, gas-particle partitioning theory and the analytical techniques used to determine the chemical composition of SOA. A survey of recent laboratory, field and modeling studies is also presented. The following topical and emerging issues are highlighted and discussed in detail: molecular characterization of biogenic SOA constituents, condensed phase reactions and oligomerization, the interaction of atmospheric organic components with sulfuric acid, the chemical and photochemical processing of organics in the atmospheric aqueous phase, aerosol formation from real plant emissions, interaction of atmospheric organic components with water, thermodynamics and mixtures in atmospheric models. Finally, the major challenges ahead in laboratory, field and modeling studies of SOA are discussed and recommendations for future research directions are proposed.

Abstract When surrounded by a transparent emission region, black holes are expected to reveal a dark shadow caused by gravitational light bending and photon capture at the event horizon. To image and study this phenomenon, we have assembled the Event Horizon Telescope, a global very long baseline interferometry array observing at a wavelength of 1.3 mm. This allows us to reconstruct event-horizon-scale images of the supermassive black hole candidate in the center of the giant elliptical galaxy M87. We have resolved the central compact radio source as an asymmetric bright emission ring with a diameter of 42 ± 3 μ as, which is circular and encompasses a central depression in brightness with a flux ratio ≳10:1. The emission ring is recovered using different calibration and imaging schemes, with its diameter and width remaining stable over four different observations carried out in different days. Overall, the observed image is consistent with expectations for the shadow of a Kerr black hole as predicted by general relativity. The asymmetry in brightness in the ring can be explained in terms of relativistic beaming of the emission from a plasma rotating close to the speed of light around a black hole. We compare our images to an extensive library of ray-traced general-relativistic magnetohydrodynamic simulations of black holes and derive a central mass of M = (6.5 ± 0.7) × 10 9 M ⊙ . Our radio-wave observations thus provide powerful evidence for the presence of supermassive black holes in centers of galaxies and as the central engines of active galactic nuclei. They also present a new tool to explore gravity in its most extreme limit and on a mass scale that was so far not accessible.

Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to ∼80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

The aim of this paper is to advocate the usefulness of the spin-density-functional (SDF) formalism. The generalization of the Hohenberg-Kohn-Sham scheme to and SDF formalism is presented in its thermodynamic version. The ground-state formalism is extended to more general Hamiltonians and to the lowest excited state of each symmetry. A relation between the exchange-correlation functional and the pair correlation function is derived. It is used for the interpretation of approximate versions of the theory, in particular the local-spin-density (LSD) approximation, which is formally valid only in the limit of slow and weak spatial variation in the density. It is shown, however, to give good account for the exchange-correlation energy also in rather inhomogeneous situations, because only the spherical average of the exchange-correlation hole influences this energy, and because it fulfills the sum rule stating that this hole should contain only one charge unit. A further advantage of the LSD approximation is that it can be systematically improved. Calculations on the homogeneous spin-polarized electron liquid are reported on. These calculations provide data in the form of interpolation formulas for the exchange-correlation energy and potentials, to be used in the LSD approximation. The ground-state properties are obtained from the Galitskii-Migdal formula, which relates the total energy to the one-electron spectrum, obtained with a dynamical self-energy. The self-energy is calculated in an electron-plasmon model where the electron is assumed to couple to one single mode. The potential for excited states is obtained by identifying the quasiparticle peak in the spectrum. Correlation is found to significantly weaken the spin dependence of the potentials, compared with the result in the Hartree-Fock approximation. Charge and spin response functions are calculated in the long-wavelength limit. Correlation is found to be very important for properties which involve a change in the spinpolarization. For atoms, molecules, and solids the usefulness of the SDF formalism is discussed. In order to explore the range of applicability, a few applications of the LSD approximation are made on systems for which accurate solutions exist. The calculated ionization potentials, affinities, and excitation energies for atoms propose that the valence electrons are fairly well described, a typical error in the ionization energy being 1/2 eV. The exchange-correlation holes of two-electron ions are discussed. An application to the hydrogen molecule, using a minimum basis set, shows that the LSD approximation gives good results for the energy curve for all separations studied, in contrast to the spin-independent local approximation. In particular, the error in the binding energy is only 0.1 eV, and bond breaking is properly described. For solids, the SDF formalism provides a framework for band models of magnetism. An estimate of the splitting between spin-up and spin-down energy bands of a ferromagnetic transition metal shows that the LSD approximation gives a correction of the correct sign and order of magnitude to published $X\ensuremath{\alpha}$ results. To stimulate further use of the SDF formalism in the LSD approximation, the paper is self-contained and describes the necessary formulas and input data for the potentials.

Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.

We propose a second version of the van der Waals density functional of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)], employing a more accurate semilocal exchange functional and the use of a large-$N$ asymptote gradient correction in determining the vdW kernel. The predicted binding energy, equilibrium separation, and potential-energy curve shape are close to those of accurate quantum chemical calculations on 22 duplexes. We anticipate the enabling of chemically accurate calculations in sparse materials of importance for condensed matter, surface, chemical, and biological physics.

LOFAR, the LOw-Frequency ARray, is a new-generation radio interferometer constructed in the north of the Netherlands and across europe. Utilizing a novel phased-array design, LOFAR covers the largely unexplored low-frequency range from 10–240 MHz and provides a number of unique observing capabilities. Spreading out from a core located near the village of Exloo in the northeast of the Netherlands, a total of 40 LOFAR stations are nearing completion. A further five stations have been deployed throughout Germany, and one station has been built in each of France, Sweden, and the UK. Digital beam-forming techniques make the LOFAR system agile and allow for rapid repointing of the telescope as well as the potential for multiple simultaneous observations. With its dense core array and long interferometric baselines, LOFAR achieves unparalleled sensitivity and angular resolution in the low-frequency radio regime. The LOFAR facilities are jointly operated by the International LOFAR Telescope (ILT) foundation, as an observatory open to the global astronomical community. LOFAR is one of the first radio observatories to feature automated processing pipelines to deliver fully calibrated science products to its user community. LOFAR’s new capabilities, techniques and modus operandi make it an important pathfinder for the Square Kilometre Array (SKA). We give an overview of the LOFAR instrument, its major hardware and software components, and the core science objectives that have driven its design. In addition, we present a selection of new results from the commissioning phase of this new radio observatory.

Ferroelectric smectic C (FSC) liquid crystals are used in a simple new geometry that allows the spontaneous formation of either of two surface-stabilized smectic C monodomains of opposite ferroelectric polarization. These domains are separated by well-defined walls which may be manipulated with an applied electric field. The resulting electro-optic effects exhibit a unique combination of properties: microsecond dynamics, threshold behavior, symmetric bistability, and a large electro-optic response.

We demonstrate the detection of molecular vibrations in single hemoglobin (Hb) protein molecules attached to isolated and immobilized silver nanoparticles by surface enhanced Raman scattering (SERS). A comparison between calculation and experiment indicates that electromagnetic field effects dominate the surface enhancement, and that single molecule Hb SERS is possible only for molecules situated between Ag particles. The vibrational spectra exhibit temporal fluctuations of unknown origin which appear to be characteristic of the single molecule detection limit.

We review work on In2O3:Sn films prepared by reactive e-beam evaporation of In2O3 with up to 9 mol % SnO2 onto heated glass. These films have excellent spectrally selective properties when the deposition rate is ∼0.2 nm/s, the substrate temperature is ≳150 °C, and the oxygen pressure is ∼5×10−4 Torr. Optimized coatings have crystallite dimensions ≳50 nm and a C-type rare-earth oxide structure. We cover electromagnetic properties as recorded by spectrophotometry in the 0.2–50-μm range, by X-band microwave reflectance, and by dc electrical measurements. Hall-effect data are included. An increase of the Sn content is shown to have several important effects: the semiconductor band gap is shifted towards the ultraviolet, the luminous transmittance remains high, the infrared reflectance increases to a high value beyond a certain wavelength which shifts towards the visible, phonon-induced infrared absorption bands vanish, the microwave reflectance goes up, and the dc resisitivity drops to ∼2×10−4 Ω cm. The corresponding mobility is ∼30 cm2/V s. The complex dielectric function ε is reported. These data were obtained from carefully selected combinations of spectrophotometric transmittance and reflectance data. It is found that ε can be reconciled with the Drude theory only by assuming a strongly frequency-dependent relaxation energy between the plasma energy and the band gap. We review a recently formulated quantitative theoretical model for the optical properties which explicitly includes the additive contributions to ε from valence electrons, free electrons, and phonons. The theory embodies an effective-mass model for n-doped semiconductors well above the Mott critical density. Because of the high doping, the Sn impurities are singly ionized and the associated electrons occupy the bottom of the conduction band in the form of an electron gas. The Sn ions behave approximately as point scatterers, which is consistent with pseudopotential arguments. Screening of the ions is described by the random phase approximation. This latter theory works well as a consequence of the small effective electron radii. Exchange and correlation in the electron gas are represented by the Hubbard and Singwi–Sjölander schemes. Phonon effects are included by three empirically determined damped Lorentz oscillators. Free-electron properties are found to govern the optical performance in the main spectral range. An analysis of the complex dynamic resistivity (directly related to ε) shows unambiguously that Sn ions are the most important scatterers, although grain-boundary scattering can play some role in the midvisible range. As a result of this analysis one concludes that the optical properties of the best films approach the theoretical limit. Band-gap shifts can be understood as the net result of two competing mechanisms: a widening due to the Burstein–Moss effect, and a narrowing due to electron-electron and electron-ion scattering. The transition width—including an Urbach tail—seems to be consistent with these notions. Window applications are treated theoretically from detailed computations of integrated luminous, solar, and thermal properties. It is found that In2O3:Sn films on glass can yield∼78% normal solar transmittance and ∼20% hemispherical thermal emittance. Substrate emission is found to be insignificant. Antireflection with evaporated MgF2 or high-rate sputtered aluminum oxyfluoride can give ∼95% normal luminous transmittance, ∼5% normal luminous reflectance, little perceived color and little increase in emittance. A color purity <1% in normal transmission and <10% in normal reflection is achievable for a daylight illuminant within extended ranges of film thickness.

In recent years, Carbon Capture and Storage (Sequestration) (CCS) has been proposed as a potential method to allow the continued use of fossil-fuelled power stations whilst preventing emissions of CO2 from reaching the atmosphere. Gas, coal (and biomass)-fired power stations can respond to changes in demand more readily than many other sources of electricity production, hence the importance of retaining them as an option in the energy mix. Here, we review the leading CO2 capture technologies, available in the short and long term, and their technological maturity, before discussing CO2 transport and storage. Current pilot plants and demonstrations are highlighted, as is the importance of optimising the CCS system as a whole. Other topics briefly discussed include the viability of both the capture of CO2 from the air and CO2 reutilisation as climate change mitigation strategies. Finally, we discuss the economic and legal aspects of CCS.

Provides insight in to the mathematics of Galerkin finite element method as applied to parabolic equations. This second edition covers two chapters that deal with problems in polygonal, particularly noncovex, spatial domains, and with time discretization based on using Laplace transformation and quadrature.

Hydrothermal technologies are broadly defined as chemical and physical transformations in high-temperature (200–600 °C), high-pressure (5–40 MPa) liquid or supercritical water. This thermochemical means of reforming biomass may have energetic advantages, since, when water is heated at high pressures a phase change to steam is avoided which avoids large enthalpic energy penalties. Biological chemicals undergo a range of reactions, including dehydration and decarboxylation reactions, which are influenced by the temperature, pressure, concentration, and presence of homogeneous or heterogeneous catalysts. Several biomass hydrothermal conversion processes are in development or demonstration. Liquefaction processes are generally lower temperature (200–400 °C) reactions which produce liquid products, often called “bio-oil” or “bio-crude”. Gasification processes generally take place at higher temperatures (400–700 °C) and can produce methane or hydrogen gases in high yields.