scispace - formally typeset
Search or ask a question

Showing papers by "Technical University of Denmark published in 2012"


Journal ArticleDOI
TL;DR: Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development.
Abstract: Background Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. Methods To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression. Results Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors. Conclusions Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.)

6,672 citations


Journal ArticleDOI
TL;DR: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created, and the method was evaluated on WGS chromosomes and plasmids of 30 isolates.
Abstract: Objectives Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. Thus, the current challenge is to extract the relevant information from the large amount of generated data.

3,956 citations


Book
22 Dec 2012
TL;DR: In this paper, model-based analysis and design methods for fault diagnosis and fault-tolerant control are presented, where the propagation of the fault through the process, test fault detectability and reveal redundancies that can be used to ensure fault tolerance.
Abstract: This book presents model-based analysis and design methods for fault diagnosis and fault-tolerant control. Architectural and structural models are used to analyse the propagation of the fault through the process, test fault detectability and reveal redundancies that can be used to ensure fault tolerance. Case studies demonstrate the methods presented. The second edition includes new material on reconfigurable control, diagnosis of nonlinear systems, and remote diagnosis, plus new examples and updated bibliography.

2,677 citations


Journal ArticleDOI
TL;DR: A Web-based method for MLST of 66 bacterial species based on whole-genome sequencing data that enables investigators to determine the sequence types of their isolates on the basis of WGS data.
Abstract: Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the “gold standard” of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

1,620 citations


Journal ArticleDOI
TL;DR: The potential for furthering medical research and clinical care using EHR data and the challenges that must be overcome before this is a reality are considered.
Abstract: The adoption of electronic health records will provide a rich resource for biomedical researchers. This Review discusses the potential for their use in informed decision making in the clinic, for a finer understanding of genotype–phenotype relationships and for selection of research cohorts, along with the current challenges for their mining and use. Clinical data describing the phenotypes and treatment of patients represents an underused data source that has much greater research potential than is currently realized. Mining of electronic health records (EHRs) has the potential for establishing new patient-stratification principles and for revealing unknown disease correlations. Integrating EHR data with genetic data will also give a finer understanding of genotype–phenotype relationships. However, a broad range of ethical, legal and technical reasons currently hinder the systematic deposition of these data in EHRs and their mining. Here, we consider the potential for furthering medical research and clinical care using EHR data and the challenges that must be overcome before this is a reality.

1,376 citations


Journal ArticleDOI
TL;DR: The developments in stability/degradation of OPVs in the last five years are reviewed, such as inverted device structures of the bulk heterojunction geometry device, which allows for more stable metal electrodes, the choice of more photostable active materials, the introduction of interfacial layers, and roll-to-roll fabrication.
Abstract: Organic photovoltaics (OPVs) evolve in an exponential manner in the two key areas of efficiency and stability. The power conversion efficiency (PCE) has in the last decade been increased by almost a factor of ten approaching 10%. A main concern has been the stability that was previously measured in minutes, but can now, in favorable circumstances, exceed many thousands of hours. This astonishing achievement is the subject of this article, which reviews the developments in stability/degradation of OPVs in the last five years. This progress has been gained by several developments, such as inverted device structures of the bulk heterojunction geometry device, which allows for more stable metal electrodes, the choice of more photostable active materials, the introduction of interfacial layers, and roll-to-roll fabrication, which promises fast and cheap production methods while creating its own challenges in terms of stability.

1,258 citations


Journal ArticleDOI
31 Aug 2012-Science
TL;DR: Multidrug-resistant soil bacteria containing resistance cassettes against five classes of antibiotics are described that have perfect nucleotide identity to genes from diverse human pathogens, offering not only evidence of lateral exchange but also a mechanism by which antibiotic resistance disseminates.
Abstract: Soil microbiota represent one of the ancient evolutionary origins of antibiotic resistance and have been proposed as a reservoir of resistance genes available for exchange with clinical pathogens. Using a high-throughput functional metagenomic approach in conjunction with a pipeline for the de novo assembly of short-read sequence data from functional selections (termed PARFuMS), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pathogens. We describe multidrug-resistant soil bacteria containing resistance cassettes against five classes of antibiotics (β-lactams, aminoglycosides, amphenicols, sulfonamides, and tetracyclines) that have perfect nucleotide identity to genes from diverse human pathogens. This identity encompasses noncoding regions as well as multiple mobilization sequences, offering not only evidence of lateral exchange but also a mechanism by which antibiotic resistance disseminates.

1,254 citations


Journal ArticleDOI
30 Nov 2012-Science
TL;DR: There is good agreement between different satellite methods—especially in Greenland and West Antarctica—and that combining satellite data sets leads to greater certainty, and the mass balance of Earth’s polar ice sheets is estimated by combining the results of existing independent techniques.
Abstract: We combined an ensemble of satellite altimetry, interferometry, and gravimetry data sets using common geographical regions, time intervals, and models of surface mass balance and glacial isostatic adjustment to estimate the mass balance of Earth’s polar ice sheets. We find that there is good agreement between different satellite methods—especially in Greenland and West Antarctica—and that combining satellite data sets leads to greater certainty. Between 1992 and 2011, the ice sheets of Greenland, East Antarctica, West Antarctica, and the Antarctic Peninsula changed in mass by –142 ± 49, +14 ± 43, –65 ± 26, and –20 ± 14 gigatonnes year−1, respectively. Since 1992, the polar ice sheets have contributed, on average, 0.59 ± 0.20 millimeter year−1 to the rate of global sea-level rise.

1,215 citations


Journal ArticleDOI
TL;DR: In this paper, the authors present the electrocatalytic properties of a highly conductive MoS2 hybrid material, and demonstrate that the origin of the HER activity is closely related to the amount of edges in the layered MOS2.
Abstract: This perspective covers the use of molybdenum disulfide and related compounds, generally termed MoSx, as electro- or photoelectrocatalysts for the hydrogen evolution reaction (HER). State of the art solutions as well as the most illustrative results from the extensive electro- and photoelectrocatalytic literature are given. The research strategies currently employed in the field are outlined and future challenges pointed out. We suggest that the key to optimising the HER activity of MoS2 is divided into (1) increasing the catalytic activity of the active site, (2) increasing the number of active sites of the catalyst, and (3) improving the electrical contact to these sites. These postulations are substantiated by examples from the existing literature and some new results. To demonstrate the electrocatalytic properties of a highly conductive MoS2 hybrid material, we present the HER activity data for multi-wall MoS2 nanotubes on multi-wall carbon nanotubes (MWMoS2@MWCNTs). This exemplifies the typical data collected for the electrochemical HER. In addition, it demonstrates that the origin of the activity is closely related to the amount of edges in the layered MoS2. The photoelectrocatalytic HER is also discussed, based on examples from literature, with an emphasis on the use of MoSx as either (1) the co-catalyst providing the HER activity for a semiconductor, e.g. Mo3S+4on Si or (2) MoS2 as the semiconductor with an intrinsic HER activity. Finally, suggestions for future catalyst designs are given.

1,189 citations


Journal ArticleDOI
TL;DR: In this paper, a semi-empirical density functional optimization method using regularization and cross-validation methods from machine learning is developed to avoid the overfitting found when standard least-squares methods are applied to high-order polynomial expansions.
Abstract: A methodology for semiempirical density functional optimization, using regularization and cross-validation methods from machine learning, is developed. We demonstrate that such methods enable well-behaved exchange-correlation approximations in very flexible model spaces, thus avoiding the overfitting found when standard least-squares methods are applied to high-order polynomial expansions. A general-purpose density functional for surface science and catalysis studies should accurately describe bond breaking and formation in chemistry, solid state physics, and surface chemistry, and should preferably also include van der Waals dispersion interactions. Such a functional necessarily compromises between describing fundamentally different types of interactions, making transferability of the density functional approximation a key issue. We investigate this trade-off between describing the energetics of intramolecular and intermolecular, bulk solid, and surface chemical bonding, and the developed optimization method explicitly handles making the compromise based on the directions in model space favored by different materials properties. The approach is applied to designing the Bayesian error estimation functional with van der Waals correlation (BEEF--vdW), a semilocal approximation with an additional nonlocal correlation term. Furthermore, an ensemble of functionals around BEEF--vdW comes out naturally, offering an estimate of the computational error. An extensive assessment on a range of data sets validates the applicability of BEEF--vdW to studies in chemistry and condensed matter physics. Applications of the approximation and its Bayesian ensemble error estimate to two intricate surface science problems support this.

1,071 citations


Journal ArticleDOI
TL;DR: Density functional theory calculations were used in combination with the computational standard hydrogen electrode to calculate the free energy profile for the reduction of N(2) admolecules and N adatoms on several close-packed and stepped transition metal surfaces in contact with an acidic electrolyte.
Abstract: Theoretical studies of the possibility of forming ammonia electrochemically at ambient temperature and pressure are presented. Density functional theory calculations were used in combination with the computational standard hydrogen electrode to calculate the free energy profile for the reduction of N(2) admolecules and N adatoms on several close-packed and stepped transition metal surfaces in contact with an acidic electrolyte. Trends in the catalytic activity were calculated for a range of transition metal surfaces and applied potentials under the assumption that the activation energy barrier scales with the free energy difference in each elementary step. The most active surfaces, on top of the volcano diagrams, are Mo, Fe, Rh, and Ru, but hydrogen gas formation will be a competing reaction reducing the faradaic efficiency for ammonia production. Since the early transition metal surfaces such as Sc, Y, Ti, and Zr bind N-adatoms more strongly than H-adatoms, a significant production of ammonia compared with hydrogen gas can be expected on those metal electrodes when a bias of -1 V to -1.5 V vs. SHE is applied. Defect-free surfaces of the early transition metals are catalytically more active than their stepped counterparts.

Journal ArticleDOI
TL;DR: In this article, the authors studied the phonon-limited mobility in intrinsic $n$-type single-layer MoS for temperatures $Tg100$ K. The mobility is weakly dependent on the carrier density.
Abstract: We study the phonon-limited mobility in intrinsic $n$-type single-layer MoS${}_{2}$ for temperatures $Tg100$ K. The materials properties including the electron-phonon interaction are calculated from first principles and the deformation potentials and Fr\"ohlich interaction in single-layer MoS${}_{2}$ are established. The calculated room-temperature mobility of $\ensuremath{\sim}$410 cm${}^{2}$V${}^{\ensuremath{-}1}$s${}^{\ensuremath{-}1}$ is found to be dominated by optical phonon scattering via intra and intervalley deformation potential couplings and the Fr\"ohlich interaction. The mobility is weakly dependent on the carrier density and follows a $\ensuremath{\mu}\ensuremath{\sim}{T}^{\ensuremath{-}\ensuremath{\gamma}}$ temperature dependence with $\ensuremath{\gamma}=1.69$ at room temperature. It is shown that a quenching of the characteristic homopolar mode, which is likely to occur in top-gated samples, increases the mobility with $\ensuremath{\sim}$70 cm${}^{2}$V${}^{\ensuremath{-}1}$s${}^{\ensuremath{-}1}$ and can be observed as a decrease in the exponent to $\ensuremath{\gamma}=1.52$. In comparison to recent experimental findings for the mobility in single-layer MoS${}_{2}$ ($\ensuremath{\sim}$200 cm${}^{2}$V${}^{\ensuremath{-}1}$s${}^{\ensuremath{-}1}$), our results indicate that mobilities close to the intrinsic phonon-limited mobility can be achieved in two-dimensional materials via dielectric engineering that effectively screens static Coulomb scattering on, e.g., charged impurities.

Journal ArticleDOI
TL;DR: In this paper, the authors provide an overview of the fundamentals underlying the reduction of oxygen on platinum and its alloys, and report the ORR activity of Pt5La for the first time, which shows a 3.5-to 4.5fold improvement in activity over Pt in the range 0.9 to 0.87 V.
Abstract: The high cost of low temperature fuel cells is to a large part dictated by the high loading of Pt required to catalyse the oxygen reduction reaction (ORR). Arguably the most viable route to decrease the Pt loading, and to hence commercialise these devices, is to improve the ORR activity of Pt by alloying it with other metals. In this perspective paper we provide an overview of the fundamentals underlying the reduction of oxygen on platinum and its alloys. We also report the ORR activity of Pt5La for the first time, which shows a 3.5- to 4.5-fold improvement in activity over Pt in the range 0.9 to 0.87 V, respectively. We employ angle resolved X-ray photoelectron spectroscopy and density functional theory calculations to understand the activity of Pt5La.

Journal ArticleDOI
TL;DR: A systematic overview of the state of the art in energy and resource efficiency increasing methods and techniques in the domain of discrete part manufacturing, with attention for the effectiveness of the available options is provided in this paper.
Abstract: A B S T R A C T This paper aims to provide a systematic overview of the state of the art in energy and resource efficiency increasing methods and techniques in the domain of discrete part manufacturing, with attention for the effectiveness of the available options. For this purpose a structured approach, distinguishing different system scale levels, is applied: starting from a unit process focus, respectively the multi-machine, factory, multi-facility and supply chain levels are covered. Determined by the research contributions reported in literature, the de facto focus of the paper is mainly on energy related aspects of manufacturing. Significant opportunities for systematic efficiency improving measures are identified and summarized in this area. 2012 CIRP.

Journal ArticleDOI
25 May 2012-Science
TL;DR: High-resolution transmission electron microscopy using a fluid cell to directly observe oriented attachment of iron oxyhydroxide nanoparticles shows strong, highly direction-specific interactions drive crystal growth via oriented attachment.
Abstract: The oriented attachment of molecular clusters and nanoparticles in solution is now recognized as an important mechanism of crystal growth in many materials, yet the alignment process and attachment mechanism have not been established. We performed high-resolution transmission electron microscopy using a fluid cell to directly observe oriented attachment of iron oxyhydroxide nanoparticles. The particles undergo continuous rotation and interaction until they find a perfect lattice match. A sudden jump to contact then occurs over less than 1 nanometer, followed by lateral atom-by-atom addition initiated at the contact point. Interface elimination proceeds at a rate consistent with the curvature dependence of the Gibbs free energy. Measured translational and rotational accelerations show that strong, highly direction-specific interactions drive crystal growth via oriented attachment.

Journal ArticleDOI
TL;DR: X-ray diffraction experiments reveal that spatial charge ordering occurs in the pseudogap state of YBa2Cu3O6.67 as discussed by the authors, which competes with high-temperature superconductivity, and their relative strengths can be tuned using a magnetic field.
Abstract: X-ray diffraction experiments reveal that spatial charge ordering occurs in the pseudogap state of YBa2Cu3O6.67. Moreover, this charge ordered state competes with high-temperature superconductivity, and their relative strengths can be tuned using a magnetic field.

Journal ArticleDOI
02 Mar 2012-Science
TL;DR: The transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature are reported, offering an initial understanding of why certain regulatory strategies may be favored during evolution of dynamic control systems.
Abstract: Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.

Journal ArticleDOI
01 Mar 2012-Mbio
TL;DR: The results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA, which appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance.
Abstract: Since its discovery in the early 2000s, methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398) has become a rapidly emerging cause of human infections, most often associated with livestock exposure. We applied whole-genome sequence typing to characterize a diverse collection of CC398 isolates (n = 89), including MRSA and methicillin-susceptible S. aureus (MSSA) from animals and humans spanning 19 countries and four continents. We identified 4,238 single nucleotide polymorphisms (SNPs) among the 89 core genomes. Minimal homoplasy (consistency index = 0.9591) was detected among parsimony-informative SNPs, allowing for the generation of a highly accurate phylogenetic reconstruction of the CC398 clonal lineage. Phylogenetic analyses revealed that MSSA from humans formed the most ancestral clades. The most derived lineages were composed predominantly of livestock-associated MRSA possessing three different staphylococcal cassette chromosome mec element (SCCmec) types (IV, V, and VII-like) including nine subtypes. The human-associated isolates from the basal clades carried phages encoding human innate immune modulators that were largely missing among the livestock-associated isolates. Our results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA. The lineage appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance. Further analyses are required to estimate the number of independent genetic events leading to the methicillin-resistant sublineages, but the diversity of SCCmec subtypes is suggestive of strong and diverse antimicrobial selection associated with food animal production. IMPORTANCE Modern food animal production is characterized by densely concentrated animals and routine antibiotic use, which may facilitate the emergence of novel antibiotic-resistant zoonotic pathogens. Our findings strongly support the idea that livestock-associated MRSA CC398 originated as MSSA in humans. The jump of CC398 from humans to livestock was accompanied by the loss of phage-carried human virulence genes, which likely attenuated its zoonotic potential, but it was also accompanied by the acquisition of tetracycline and methicillin resistance. Our findings exemplify a bidirectional zoonotic exchange and underscore the potential public health risks of widespread antibiotic use in food animal production.

Journal ArticleDOI
TL;DR: The theory of the acoustic radiation force is presented; a second-order, time-averaged effect responsible for the acoustophoretic motion of suspended, micrometre-sized particles in an ultrasound field.
Abstract: In this paper, Part 7 of the thematic tutorial series “Acoustofluidics – exploiting ultrasonic standing waves, forces and acoustic streaming in microfluidic systems for cell and particle manipulation ”, we present the theory of the acoustic radiation force; a second-order, time-averaged effect responsible for the acoustophoretic motion of suspended, micrometre-sized particles in an ultrasound field.

Journal ArticleDOI
TL;DR: This work discusses how P. aeruginosa evolves from a state of early, recurrent intermittent colonization of the airways of patients with CF to a chronic infection state, and how this process offers opportunities to study bacterial evolution in natural environments.
Abstract: The airways of patients with cystic fibrosis (CF) are nearly always infected with many different microorganisms. This environment offers warm, humid and nutrient-rich conditions, but is also stressful owing to frequent antibiotic therapy and the host immune response. Pseudomonas aeruginosa is commonly isolated from the airways of patients with CF, where it most often establishes chronic infections that usually persist for the rest of the lives of the patients. This bacterium is a major cause of mortality and morbidity and has therefore been studied intensely. Here, we discuss how P. aeruginosa evolves from a state of early, recurrent intermittent colonization of the airways of patients with CF to a chronic infection state, and how this process offers opportunities to study bacterial evolution in natural environments. We believe that such studies are valuable not only for our understanding of bacterial evolution but also for the future development of new therapeutic strategies to treat severe chronic infections.

Journal ArticleDOI
TL;DR: An updated inventory of microorganisms used in food fermentations covering a wide range of food matrices and the taxonomy is reviewed and updated in order to bring theTaxonomy in agreement with the current standing in nomenclature.

Journal ArticleDOI
01 Jul 2012-Boreas
TL;DR: In this paper, the authors proposed a post-IR IRSL (IRSL) method for the dating of Middle and Late Pleistocene sediments, which appears to avoid signal instability.
Abstract: Luminescence dating is used extensively to provide absolute chronologies for Late Pleistocene sediments. Nowadays, most optical dates are based on quartz optically stimulated luminescence (OSL). However, the application of this signal is usually limited to the last ∼100 ka because of saturation of the quartz luminescence signal with dose. In contrast, the feldspar infrared stimulated luminescence (IRSL) dose–response curve grows to much higher doses; this has the potential to extend the datable age range by a factor of 4–5 compared with quartz OSL. However, it has been known for several decades that this IRSL signal is unstable, and this instability often gives rise to significant age underestimation. Here we test against independent age control the recently developed feldspar post-IR IRSL approach to the dating of sediments, which appears to avoid signal instability. A physical model explaining our observations is discussed, and the method is shown to be accurate back to 600 ka. The post-IR IRSL signal is reduced by exposure to daylight more slowly than that from quartz and low-temperature IRSL, preventing its general application to young (e.g. Holocene) sediments. Nevertheless, this new approach is widely applicable (feldspar of appropriate luminescence behaviour is even more ubiquitous than quartz). These characteristics make this a method of great importance for the dating of Middle and Late Pleistocene deposits.


Journal ArticleDOI
TL;DR: It is found that a copper nanoparticle covered electrode shows better selectivity towards hydrocarbons compared with the two other studied surfaces, an electropolished copper electrode and an argon sputtered copper electrode.
Abstract: This communication examines the effect of the surface morphology of polycrystalline copper on electroreduction of CO2. We find that a copper nanoparticle covered electrode shows better selectivity towards hydrocarbons compared with the two other studied surfaces, an electropolished copper electrode and an argon sputtered copper electrode. Density functional theory calculations provide insight into the surface morphology effect.

Journal ArticleDOI
TL;DR: An updated version of the DiscoTope method incorporating a novel spatial neighborhood definition and half-sphere exposure as surface measure is presented, demonstrating that given proper benchmark definitions, B-cell epitope prediction methods achieve highly significant predictive performances suggesting these tools to be a powerful asset in rational epitope discovery.
Abstract: The interaction between antibodies and antigens is one of the most important immune system mechanisms for clearing infectious organisms from the host. Antibodies bind to antigens at sites referred to as B-cell epitopes. Identification of the exact location of B-cell epitopes is essential in several biomedical applications such as; rational vaccine design, development of disease diagnostics and immunotherapeutics. However, experimental mapping of epitopes is resource intensive making in silico methods an appealing complementary approach. To date, the reported performance of methods for in silico mapping of B-cell epitopes has been moderate. Several issues regarding the evaluation data sets may however have led to the performance values being underestimated: Rarely, all potential epitopes have been mapped on an antigen, and antibodies are generally raised against the antigen in a given biological context not against the antigen monomer. Improper dealing with these aspects leads to many artificial false positive predictions and hence to incorrect low performance values. To demonstrate the impact of proper benchmark definitions, we here present an updated version of the DiscoTope method incorporating a novel spatial neighborhood definition and half-sphere exposure as surface measure. Compared to other state-of-the-art prediction methods, Discotope-2.0 displayed improved performance both in cross-validation and in independent evaluations. Using DiscoTope-2.0, we assessed the impact on performance when using proper benchmark definitions. For 13 proteins in the training data set where sufficient biological information was available to make a proper benchmark redefinition, the average AUC performance was improved from 0.791 to 0.824. Similarly, the average AUC performance on an independent evaluation data set improved from 0.712 to 0.727. Our results thus demonstrate that given proper benchmark definitions, B-cell epitope prediction methods achieve highly significant predictive performances suggesting these tools to be a powerful asset in rational epitope discovery. The updated version of DiscoTope is available at www.cbs.dtu.dk/services/DiscoTope-2.0.

Journal ArticleDOI
TL;DR: In this paper, a review of the possible mechanisms for self-healing phenomenon in cementitious materials, which are summarized based on substantial experimental studies and practical experience, are reviewed.

Book ChapterDOI
02 Dec 2012
TL;DR: In this paper, a block cipher called PRINCE is proposed that allows encryption of data within one clock cycle with a very competitive chip area compared to known solutions. But it does not have the α-reflection property, which holds that decryption for one key corresponds to encryption with another key.
Abstract: This paper presents a block cipher that is optimized with respect to latency when implemented in hardware. Such ciphers are desirable for many future pervasive applications with real-time security needs. Our cipher, named PRINCE, allows encryption of data within one clock cycle with a very competitive chip area compared to known solutions. The fully unrolled fashion in which such algorithms need to be implemented calls for innovative design choices. The number of rounds must be moderate and rounds must have short delays in hardware. At the same time, the traditional need that a cipher has to be iterative with very similar round functions disappears, an observation that increases the design space for the algorithm. An important further requirement is that realizing decryption and encryption results in minimum additional costs. PRINCE is designed in such a way that the overhead for decryption on top of encryption is negligible. More precisely for our cipher it holds that decryption for one key corresponds to encryption with a related key. This property we refer to as α-reflection is of independent interest and we prove its soundness against generic attacks.

Journal ArticleDOI
TL;DR: The observation of destructive quantum interference in charge transport through two-terminal molecular junctions at room temperature is reported, and the degree of interference can be controlled by simple chemical modifications of the molecular wire.
Abstract: As the dimensions of a conductor approach the nanoscale, quantum effects begin to dominate, and it becomes possible to control the conductance through direct manipulation of the electron wavefunction. Such control has been demonstrated in various mesoscopic devices at cryogenic temperatures, but it has proved to be difficult to exert control over the wavefunction at higher temperatures. Molecules have typical energy level spacings (∼eV) that are much larger than the thermal energy at 300 K (∼25 meV), and are therefore natural candidates for such experiments. Previously, phenomena such as giant magnetoresistance, Kondo effects and conductance switching have been observed in single molecules, and theorists have predicted that it should also be possible to observe quantum interference in molecular conductors, but until now all the evidence for such behaviour has been indirect. Here, we report the observation of destructive quantum interference in charge transport through two-terminal molecular junctions at room temperature. We studied five different rigid π-conjugated molecular wires, all of which form self-assembled monolayers on a gold surface, and find that the degree of interference can be controlled by simple chemical modifications of the molecular wire.

Journal ArticleDOI
TL;DR: An integrated perspective is provided on the basis of the recent application of nanoscience approaches to nanocarrier design and engineering to establish the interdependency of nanoparticle size, shape, and surface characteristics in relation to interfacial forces.
Abstract: Intravenously injected nanoparticulate drug carriers provide a wide range of unique opportunities for site-specific targeting of therapeutic agents to many areas within the vasculature and beyond. Pharmacokinetics and biodistribution of these carriers are controlled by a complex array of interrelated core and interfacial physicochemical and biological factors. Pertinent to realizing therapeutic goals, definitive maps that establish the interdependency of nanoparticle size, shape, and surface characteristics in relation to interfacial forces, biodistribution, controlled drug release, excretion, and adverse effects must be outlined. These concepts are critically evaluated and an integrated perspective is provided on the basis of the recent application of nanoscience approaches to nanocarrier design and engineering. The future of this exciting field is bright; some regulatory-approved products are already on the market and many are in late-phase clinical trials. With concomitant advances in extensive computational knowledge of the genomics and epigenomics of interindividual variations in drug responses, the boundaries toward development of personalized nanomedicines can be pushed further.

Journal ArticleDOI
TL;DR: In this paper, a polymer solar cell was developed to address the need for daily production of 1 GWp on a global level, which does not employ elements with critically low abundance and has a low thermal budget.
Abstract: Scalability is a requirement before any new energy source can be expected to house a possible solution to the challenge that mankind’s increasing energy demand presents. No renewable energy source is as abundant as the Sun and yet efficient and low-cost conversion of solar energy still has not been developed. We approach the challenge by firstly taking a technology that efficiently addresses the need for daily production of 1 GWp on a global level, which does not employ elements with critically low abundance and has a low thermal budget. We then applied life cycle assessment methodologies to direct research and developed such technology in the form of a polymer solar cell that presents a significant improvement in energy payback time (EPBT) and found that very short energy payback times on the order of one day are possible, thus potentially presenting a solution to the current energy gap of >14 TW by year 2050.