@article{809,
  abstract     = {The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position.},
  author       = {Bharata, Tanmay A and Menendez, Luis R and Hagena, Wim J and Luxd, Vanda and Igonete, Sebastien and Schorba, Martin and Florian Schur and Kraüsslich, Hans Georg and Briggsa, John A},
  journal      = {PNAS},
  number       = {22},
  pages        = {8233 -- 8238},
  publisher    = {National Academy of Sciences},
  title        = {{Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly}},
  doi          = {10.1073/pnas.1401455111},
  volume       = {111},
  year         = {2014},
}

@article{8244,
  abstract     = {Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer.},
  author       = {Singer, J. and Fazekas, Judit and Wang, W. and Weichselbaumer, M. and Matz, M. and Mader, A. and Steinfellner, W. and Meitz, S. and Mechtcheriakova, D. and Sobanov, Y. and Willmann, M. and Stockner, T. and Spillner, E. and Kunert, R. and Jensen-Jarolim, E.},
  issn         = {1535-7163},
  journal      = {Molecular Cancer Therapeutics},
  number       = {7},
  pages        = {1777--1790},
  publisher    = {American Association for Cancer Research},
  title        = {{Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients}},
  doi          = {10.1158/1535-7163.mct-13-0288},
  volume       = {13},
  year         = {2014},
}

@article{845,
  abstract     = {Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.},
  author       = {Seplyarskiy, Vladimir B and Logacheva, Maria D and Penin, Aleksey A and Baranová, Maria A and Leushkin, Evgeny V and Demidenko, Natalia V and Klepikova, Anna V and Fyodor Kondrashov and Kondrashov, Alexey S and James, Timothy Y},
  journal      = {Molecular Biology and Evolution},
  number       = {11},
  pages        = {3016 -- 3025},
  publisher    = {Oxford University Press},
  title        = {{Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity}},
  doi          = {10.1093/molbev/msu242},
  volume       = {31},
  year         = {2014},
}

@article{8458,
  abstract     = {The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.},
  author       = {Schanda, Paul and Triboulet, Sébastien and Laguri, Cédric and Bougault, Catherine M. and Ayala, Isabel and Callon, Morgane and Arthur, Michel and Simorre, Jean-Pierre},
  issn         = {0002-7863},
  journal      = {Journal of the American Chemical Society},
  number       = {51},
  pages        = {17852--17860},
  publisher    = {American Chemical Society},
  title        = {{Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan}},
  doi          = {10.1021/ja5105987},
  volume       = {136},
  year         = {2014},
}

@article{8459,
  abstract     = {Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis.},
  author       = {Morin, Sébastien and Linnet, Troels E and Lescanne, Mathilde and Schanda, Paul and Thompson, Gary S and Tollinger, Martin and Teilum, Kaare and Gagné, Stéphane and Marion, Dominique and Griesinger, Christian and Blackledge, Martin and d’Auvergne, Edward J},
  issn         = {1367-4803},
  journal      = {Bioinformatics},
  keywords     = {Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications},
  number       = {15},
  pages        = {2219--2220},
  publisher    = {Oxford University Press},
  title        = {{Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data}},
  doi          = {10.1093/bioinformatics/btu166},
  volume       = {30},
  year         = {2014},
}

@article{8460,
  abstract     = {The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states.},
  author       = {Ma, Peixiang and Haller, Jens D. and Zajakala, Jérémy and Macek, Pavel and Sivertsen, Astrid C. and Willbold, Dieter and Boisbouvier, Jérôme and Schanda, Paul},
  issn         = {1433-7851},
  journal      = {Angewandte Chemie International Edition},
  number       = {17},
  pages        = {4312--4317},
  publisher    = {Wiley},
  title        = {{Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy}},
  doi          = {10.1002/anie.201311275},
  volume       = {53},
  year         = {2014},
}

@article{8500,
  abstract     = {The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way.},
  author       = {Kaloshin, Vadim and Levi, Mark and Saprykina, Maria},
  issn         = {0010-3640},
  journal      = {Communications on Pure and Applied Mathematics},
  keywords     = {Applied Mathematics, General Mathematics},
  number       = {5},
  pages        = {748--775},
  publisher    = {Wiley},
  title        = {{Arnol′d diffusion in a pendulum lattice}},
  doi          = {10.1002/cpa.21509},
  volume       = {67},
  year         = {2014},
}

@article{8501,
  abstract     = {In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation.},
  author       = {Bounemoura, Abed and Kaloshin, Vadim},
  issn         = {1609-3321},
  journal      = {Moscow Mathematical Journal},
  keywords     = {General Mathematics},
  number       = {2},
  pages        = {181--203},
  publisher    = {Independent University of Moscow},
  title        = {{Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom}},
  doi          = {10.17323/1609-4514-2014-14-2-181-203},
  volume       = {14},
  year         = {2014},
}

@article{852,
  abstract     = {Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. },
  author       = {Rosello, Oriol P and Fyodor Kondrashov},
  journal      = {Genome Biology and Evolution},
  number       = {8},
  pages        = {1949 -- 1955},
  publisher    = {Oxford University Press},
  title        = {{Long-Term asymmetrical acceleration of protein evolution after gene duplication}},
  doi          = {10.1093/gbe/evu159},
  volume       = {6},
  year         = {2014},
}

@article{856,
  abstract     = {The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network.},
  author       = {Pougach, Ksenia S and Voet, Arnout R and Fyodor Kondrashov and Voordeckers, Karin and Christiaens, Joaquin F and Baying, Bianka and Bénès, Vladimı́r and Sakai, Ryo and Aerts, Jan A and Zhu, Bo and Van Dijck, Patrick and Verstrepen, Kevin J},
  journal      = {Nature Communications},
  publisher    = {Nature Publishing Group},
  title        = {{Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network}},
  doi          = {10.1038/ncomms5868},
  volume       = {5},
  year         = {2014},
}

@article{863,
  abstract     = {The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.},
  author       = {Moroz, Leonid L and Kocot, Kevin M and Citarella, Mathew R and Dosung, Sohn and Norekian, Tigran P and Povolotskaya, Inna and Grigorenko, Anastasia P and Dailey, Christopher A and Berezikov, Eugene and Buckley, Katherine M and Ptitsyn, Andrey A and Reshetov, Denis A and Mukherjee, Krishanu and Moroz, Tatiana P and Bobkova, Yelena V and Yu, Fahong and Kapitonov, Vladimir V and Jurka, Jerzy W and Bobkov, Yuriy V and Swore, Joshua J and Girardo, David O and Fodor, Alexander and Gusev, Fedor E and Sanford, Rachel S and Bruders, Rebecca and Kittler, Ellen L and Mills, Claudia E and Rast, Jonathan P and Derelle, Romain and Solovyev, Victor and Fyodor Kondrashov and Swalla, Billie J and Sweedler, Jonathan V and Rogaev, Evgeny I and Halanych, Kenneth M and Kohn, Andrea B},
  journal      = {Nature},
  number       = {7503},
  pages        = {109 -- 114},
  publisher    = {Nature Publishing Group},
  title        = {{The ctenophore genome and the evolutionary origins of neural systems}},
  doi          = {10.1038/nature13400},
  volume       = {510},
  year         = {2014},
}

@article{865,
  abstract     = {Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers.},
  author       = {Koval, Alexey V and Vlasov, Peter K and Shichkova, Polina and Khunderyakova, S and Markov, Yury and Panchenko, J and Volodina, A and Fyodor Kondrashov and Katanaev, Vladimir L},
  journal      = {Biochemical Pharmacology},
  number       = {4},
  pages        = {571 -- 578},
  publisher    = {Elsevier},
  title        = {{Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling}},
  doi          = {10.1016/j.bcp.2013.12.007},
  volume       = {87},
  year         = {2014},
}

@article{892,
  abstract     = {The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution.},
  author       = {Ivankov, Dmitry N and Finkelstein, Alexei V and Fyodor Kondrashov},
  journal      = {Current Opinion in Structural Biology},
  number       = {1},
  pages        = {104 -- 112},
  publisher    = {Elsevier},
  title        = {{A structural perspective of compensatory evolution}},
  doi          = {10.1016/j.sbi.2014.05.004},
  volume       = {26},
  year         = {2014},
}

@article{1629,
  abstract     = {We propose a method for propagating edit operations in 2D vector graphics, based on geometric relationship functions. These functions quantify the geometric relationship of a point to a polygon, such as the distance to the boundary or the direction to the closest corner vertex. The level sets of the relationship functions describe points with the same relationship to a polygon. For a given query point, we first determine a set of relationships to local features, construct all level sets for these relationships, and accumulate them. The maxima of the resulting distribution are points with similar geometric relationships. We show extensions to handle mirror symmetries, and discuss the use of relationship functions as local coordinate systems. Our method can be applied, for example, to interactive floorplan editing, and it is especially useful for large layouts, where individual edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds of objects by propagating relatively few edit operations.},
  author       = {Guerrero, Paul and Jeschke, Stefan and Wimmer, Michael and Wonka, Peter},
  journal      = {ACM Transactions on Graphics},
  number       = {2},
  publisher    = {ACM},
  title        = {{Edit propagation using geometric relationship functions}},
  doi          = {10.1145/2591010},
  volume       = {33},
  year         = {2014},
}

@inproceedings{1643,
  abstract     = {We extend the notion of verifiable random functions (VRF) to constrained VRFs, which generalize the concept of constrained pseudorandom functions, put forward by Boneh and Waters (Asiacrypt’13), and independently by Kiayias et al. (CCS’13) and Boyle et al. (PKC’14), who call them delegatable PRFs and functional PRFs, respectively. In a standard VRF the secret key sk allows one to evaluate a pseudorandom function at any point of its domain; in addition, it enables computation of a non-interactive proof that the function value was computed correctly. In a constrained VRF from the key sk one can derive constrained keys skS for subsets S of the domain, which allow computation of function values and proofs only at points in S. After formally defining constrained VRFs, we derive instantiations from the multilinear-maps-based constrained PRFs by Boneh and Waters, yielding a VRF with constrained keys for any set that can be decided by a polynomial-size circuit. Our VRFs have the same function values as the Boneh-Waters PRFs and are proved secure under the same hardness assumption, showing that verifiability comes at no cost. Constrained (functional) VRFs were stated as an open problem by Boyle et al.},
  author       = {Fuchsbauer, Georg},
  booktitle    = {SCN 2014},
  editor       = {Abdalla, Michel and De Prisco, Roberto},
  location     = {Amalfi, Italy},
  pages        = {95 -- 114},
  publisher    = {Springer},
  title        = {{Constrained Verifiable Random Functions }},
  doi          = {10.1007/978-3-319-10879-7_7},
  volume       = {8642},
  year         = {2014},
}

@inproceedings{1702,
  abstract     = {In this paper we present INTERHORN, a solver for recursion-free Horn clauses. The main application domain of INTERHORN lies in solving interpolation problems arising in software verification. We show how a range of interpolation problems, including path, transition, nested, state/transition and well-founded interpolation can be handled directly by INTERHORN. By detailing these interpolation problems and their Horn clause representations, we hope to encourage the emergence of a common back-end interpolation interface useful for diverse verification tools.},
  author       = {Gupta, Ashutosh and Popeea, Corneliu and Rybalchenko, Andrey},
  booktitle    = {Electronic Proceedings in Theoretical Computer Science, EPTCS},
  location     = {Vienna, Austria},
  pages        = {31 -- 38},
  publisher    = {Open Publishing},
  title        = {{Generalised interpolation by solving recursion free-horn clauses}},
  doi          = {10.4204/EPTCS.169.5},
  volume       = {169},
  year         = {2014},
}

@inproceedings{1708,
  abstract     = {It has been long argued that, because of inherent ambiguity and noise, the brain needs to represent uncertainty in the form of probability distributions. The neural encoding of such distributions remains however highly controversial. Here we present a novel circuit model for representing multidimensional real-valued distributions using a spike based spatio-temporal code. Our model combines the computational advantages of the currently competing models for probabilistic codes and exhibits realistic neural responses along a variety of classic measures. Furthermore, the model highlights the challenges associated with interpreting neural activity in relation to behavioral uncertainty and points to alternative population-level approaches for the experimental validation of distributed representations.},
  author       = {Savin, Cristina and Denève, Sophie},
  location     = {Montreal, Canada},
  number       = {January},
  pages        = {2024 -- 2032},
  publisher    = {Neural Information Processing Systems},
  title        = {{Spatio-temporal representations of uncertainty in spiking neural networks}},
  volume       = {3},
  year         = {2014},
}

@article{1733,
  abstract     = {The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a distance for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intuitively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces, and how to synthesize an interface from incompatible requirements. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies.},
  author       = {Cerny, Pavol and Chmelik, Martin and Henzinger, Thomas A and Radhakrishna, Arjun},
  journal      = {Theoretical Computer Science},
  number       = {3},
  pages        = {348 -- 363},
  publisher    = {Elsevier},
  title        = {{Interface simulation distances}},
  doi          = {10.1016/j.tcs.2014.08.019},
  volume       = {560},
  year         = {2014},
}

@article{1761,
  abstract     = {Metal silicides formed by means of thermal annealing processes are employed as contact materials in microelectronics. Control of the structure of silicide/silicon interfaces becomes a critical issue when the characteristic size of the device is reduced below a few tens of nanometers. Here, we report on silicide clustering occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling spectroscopy. Our results provide evidence for the segregation of a PtSi cluster with a diameter of a few nanometers from the silicide contact. The cluster acts as a metallic quantum dot giving rise to distinct signatures of quantum transport through its discrete energy states.},
  author       = {Mongillo, Massimo and Spathis, Panayotis N and Georgios Katsaros and De Franceschi, Silvano and Gentile, Pascal and Rurali, Riccardo and Cartoixà, Xavier},
  journal      = {Physical Review X},
  number       = {4},
  publisher    = {American Physical Society},
  title        = {{PtSi clustering in silicon probed by transport spectroscopy}},
  doi          = {10.1103/PhysRevX.3.041025},
  volume       = {3},
  year         = {2014},
}

@article{1791,
  abstract     = {Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways.},
  author       = {Baek, SeungTae and Kerjan, Géraldine and Bielas, Stephanie L and Lee, Jieun and Fenstermaker, Ali G and Gaia Novarino and Gleeson, Joseph G},
  journal      = {Neuron},
  number       = {6},
  pages        = {1255 -- 1262},
  publisher    = {Elsevier},
  title        = {{Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation}},
  doi          = {10.1016/j.neuron.2014.04.036},
  volume       = {82},
  year         = {2014},
}