@article{2226,
  abstract     = {Coriolis force effects on shear flows are important in geophysical and astrophysical contexts. We report a study on the linear stability and the transient energy growth of the plane Couette flow with system rotation perpendicular to the shear direction. External rotation causes linear instability. At small rotation rates, the onset of linear instability scales inversely with the rotation rate and the optimal transient growth in the linearly stable region is slightly enhanced ∼Re2. The corresponding optimal initial perturbations are characterized by roll structures inclined in the streamwise direction and are twisted under external rotation. At large rotation rates, the transient growth is significantly inhibited and hence linear stability analysis is a reliable indicator for instability.},
  author       = {Shi, Liang and Hof, Björn and Tilgner, Andreas},
  issn         = {15393755},
  journal      = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
  number       = {1},
  publisher    = {American Institute of Physics},
  title        = {{Transient growth of Ekman-Couette flow}},
  doi          = {10.1103/PhysRevE.89.013001},
  volume       = {89},
  year         = {2014},
}

@article{2227,
  abstract     = {The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent.},
  author       = {Cires Rodriguez, Eduardo and Baltisberger, Matthias and Cuesta, Candela and Vargas, Pablo and Prieto, José},
  issn         = {14396092},
  journal      = {Organisms Diversity and Evolution},
  number       = {1},
  pages        = {1 -- 10},
  publisher    = {Springer},
  title        = {{Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences}},
  doi          = {10.1007/s13127-013-0150-6},
  volume       = {14},
  year         = {2014},
}

@article{2228,
  abstract     = {Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing.},
  author       = {Hu, Hua and Jonas, Peter M},
  issn         = {10976256},
  journal      = {Nature Neuroscience},
  number       = {5},
  pages        = {686--693},
  publisher    = {Nature Publishing Group},
  title        = {{A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons}},
  doi          = {10.1038/nn.3678},
  volume       = {17},
  year         = {2014},
}

@article{2229,
  abstract     = {The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose "microdomain" coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity.},
  author       = {Vyleta, Nicholas and Jonas, Peter M},
  issn         = {00368075},
  journal      = {Science},
  number       = {6171},
  pages        = {665 -- 670},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse}},
  doi          = {10.1126/science.1244811},
  volume       = {343},
  year         = {2014},
}

@article{2230,
  abstract     = {Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.},
  author       = {Guzmán, José and Schlögl, Alois and Schmidt Hieber, Christoph},
  issn         = {16625196},
  journal      = {Frontiers in Neuroinformatics},
  number       = {FEB},
  publisher    = {Frontiers Research Foundation},
  title        = {{Stimfit: Quantifying electrophysiological data with Python}},
  doi          = {10.3389/fninf.2014.00016},
  volume       = {8},
  year         = {2014},
}

@article{2231,
  abstract     = {Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail.},
  author       = {Rieckh, Georg and Tkacik, Gasper},
  issn         = {00063495},
  journal      = {Biophysical Journal},
  number       = {5},
  pages        = {1194 -- 1204},
  publisher    = {Biophysical Society},
  title        = {{Noise and information transmission in promoters with multiple internal states}},
  doi          = {10.1016/j.bpj.2014.01.014},
  volume       = {106},
  year         = {2014},
}

@article{2232,
  abstract     = {The purpose of this contribution is to summarize and discuss recent advances regarding the onset of turbulence in shear flows. The absence of a clear-cut instability mechanism, the spatio-temporal intermittent character and extremely long lived transients are some of the major difficulties encountered in these flows and have hindered progress towards understanding the transition process. We will show for the case of pipe flow that concepts from nonlinear dynamics and statistical physics can help to explain the onset of turbulence. In particular, the turbulent structures (puffs) observed close to onset are spatially localized chaotic transients and their lifetimes increase super-exponentially with Reynolds number. At the same time fluctuations of individual turbulent puffs can (although very rarely) lead to the nucleation of new puffs. The competition between these two stochastic processes gives rise to a non-equilibrium phase transition where turbulence changes from a super-transient to a sustained state.},
  author       = {Song, Baofang and Hof, Björn},
  issn         = {17425468},
  journal      = {Journal of Statistical Mechanics Theory and Experiment},
  number       = {2},
  publisher    = {IOP Publishing},
  title        = {{Deterministic and stochastic aspects of the transition to turbulence}},
  doi          = {10.1088/1742-5468/2014/02/P02001},
  volume       = {2014},
  year         = {2014},
}

@article{2233,
  abstract     = { A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, valuing a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by λi, where the discount factor λ is a fixed rational number greater than 1. The value of a word is the minimal value of the automaton runs on it. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, reflecting the assumption that earlier weights are more important than later weights. Unfortunately, determinization of NDAs, which is often essential in formal verification, is, in general, not possible. We provide positive news, showing that every NDA with an integral discount factor is determinizable. We complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: for every nonintegral rational discount factor λ, there is a nondeterminizable λ-NDA. We also prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. For general NDAs, we look into approximate determinization, which is always possible as the influence of a word's suffix decays. We show that the naive approach, of unfolding the automaton computations up to a sufficient level, is doubly exponential in the discount factor. We provide an alternative construction for approximate determinization, which is singly exponential in the discount factor, in the precision, and in the number of states. We also prove matching lower bounds, showing that the exponential dependency on each of these three parameters cannot be avoided. All our results hold equally for automata over finite words and for automata over infinite words. },
  author       = {Boker, Udi and Henzinger, Thomas A},
  issn         = {18605974},
  journal      = {Logical Methods in Computer Science},
  number       = {1},
  publisher    = {International Federation of Computational Logic},
  title        = {{Exact and approximate determinization of discounted-sum automata}},
  doi          = {10.2168/LMCS-10(1:10)2014},
  volume       = {10},
  year         = {2014},
}

@article{2234,
  abstract     = {We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with κ limit-average functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the case of one limit-average function, both randomization and memory are necessary for strategies even for ε-approximation, and that finite-memory randomized strategies are sufficient for achieving Pareto optimal values. Under the satisfaction objective, in contrast to the case of one limit-average function, infinite memory is necessary for strategies achieving a specific value (i.e. randomized finite-memory strategies are not sufficient), whereas memoryless randomized strategies are sufficient for ε-approximation, for all ε > 0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be ε-approximated in time polynomial in the size of the MDP and 1/ε, and exponential in the number of limit-average functions, for all ε > 0. Our analysis also reveals flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, corrects the flaws, and allows us to obtain improved results.},
  author       = {Brázdil, Tomáš and Brožek, Václav and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín},
  issn         = {18605974},
  journal      = {Logical Methods in Computer Science},
  number       = {1},
  publisher    = {International Federation of Computational Logic},
  title        = {{Markov decision processes with multiple long-run average objectives}},
  doi          = {10.2168/LMCS-10(1:13)2014},
  volume       = {10},
  year         = {2014},
}

@article{2235,
  abstract     = {Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators.},
  author       = {Fürst, Matthias and Mcmahon, Dino and Osborne, Juliet and Paxton, Robert and Brown, Mark},
  issn         = {00280836},
  journal      = {Nature},
  number       = {7488},
  pages        = {364 -- 366},
  publisher    = {Nature Publishing Group},
  title        = {{Disease associations between honeybees and bumblebees as a threat to wild pollinators}},
  doi          = {10.1038/nature12977},
  volume       = {506},
  year         = {2014},
}

@inproceedings{2236,
  abstract     = {Consider a joint distribution (X,A) on a set. We show that for any family of distinguishers, there exists a simulator such that 1 no function in can distinguish (X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient than the functions in. For the most interesting settings of the parameters (in particular, the cryptographic case where X has superlogarithmic min-entropy, ε > 0 is negligible and consists of circuits of polynomial size), we can make the simulator h deterministic. As an illustrative application of our theorem, we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09. Our proof is simpler and quantitatively much better than the original proof using the dense model theorem, giving meaningful security guarantees if instantiated with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and Pass gave an interactive variant of our main theorem, and used it to investigate weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version of our theorem using their new uniform min-max theorem.},
  author       = {Jetchev, Dimitar and Pietrzak, Krzysztof Z},
  editor       = {Lindell, Yehuda},
  isbn         = {978-364254241-1},
  location     = {San Diego, USA},
  pages        = {566 -- 590},
  publisher    = {Springer},
  title        = {{How to fake auxiliary input}},
  doi          = {10.1007/978-3-642-54242-8_24},
  volume       = {8349},
  year         = {2014},
}

@inproceedings{2239,
  abstract     = {The analysis of the energy consumption of software is an important goal for quantitative formal methods. Current methods, using weighted transition systems or energy games, model the energy source as an ideal resource whose status is characterized by one number, namely the amount of remaining energy. Real batteries, however, exhibit behaviors that can deviate substantially from an ideal energy resource. Based on a discretization of a standard continuous battery model, we introduce battery transition systems. In this model, a battery is viewed as consisting of two parts-the available-charge tank and the bound-charge tank. Any charge or discharge is applied to the available-charge tank. Over time, the energy from each tank diffuses to the other tank. Battery transition systems are infinite state systems that, being not well-structured, fall into no decidable class that is known to us. Nonetheless, we are able to prove that the !-regular modelchecking problem is decidable for battery transition systems. We also present a case study on the verification of control programs for energy-constrained semi-autonomous robots.},
  author       = {Boker, Udi and Henzinger, Thomas A and Radhakrishna, Arjun},
  isbn         = {978-145032544-8},
  location     = {San Diego, USA},
  number       = {1},
  pages        = {595 -- 606},
  publisher    = {ACM},
  title        = {{Battery transition systems}},
  doi          = {10.1145/2535838.2535875},
  volume       = {49},
  year         = {2014},
}

@article{2240,
  abstract     = {Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is essential for physiology and development, but the identification and organization of the machinery operating this process remains largely obscure. Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. The TPLATE complex is recruited as dynamic foci at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin, and dynamin-related proteins. Reduced function of different complex components severely impaired internalization of assorted endocytic cargoes, demonstrating its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE complex is an early endocytic module representing a unique evolutionary plant adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis.},
  author       = {Gadeyne, Astrid and Sánchez Rodríguez, Clara and Vanneste, Steffen and Di Rubbo, Simone and Zauber, Henrik and Vanneste, Kevin and Van Leene, Jelle and De Winne, Nancy and Eeckhout, Dominique and Persiau, Geert and Van De Slijke, Eveline and Cannoot, Bernard and Vercruysse, Leen and Mayers, Jonathan and Adamowski, Maciek and Kania, Urszula and Ehrlich, Matthias and Schweighofer, Alois and Ketelaar, Tijs and Maere, Steven and Bednarek, Sebastian and Friml, Jirí and Gevaert, Kris and Witters, Erwin and Russinova, Eugenia and Persson, Staffan and De Jaeger, Geert and Van Damme, Daniël},
  issn         = {00928674},
  journal      = {Cell},
  number       = {4},
  pages        = {691 -- 704},
  publisher    = {Cell Press},
  title        = {{The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants}},
  doi          = {10.1016/j.cell.2014.01.039},
  volume       = {156},
  year         = {2014},
}

@article{2241,
  abstract     = {The brain demands high-energy supply and obstruction of blood flow causes rapid deterioration of the healthiness of brain cells. Two major events occur upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity. However, cellular source of glutamate and its release mechanism upon ischemia remained unknown. Here we show a causal relationship between glial acidosis and neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2 (ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular acidification. Optical activation of ChR2 expressed in glial cells led to glial acidification and to release of glutamate. On the other hand, glial alkalization via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation of glutamate release and to the relief of ischemic brain damage in vivo. Our results suggest that controlling glial pH may be an effective therapeutic strategy for intervention of ischemic brain damage.},
  author       = {Beppu, Kaoru and Sasaki, Takuya and Tanaka, Kenji and Yamanaka, Akihiro and Fukazawa, Yugo and Shigemoto, Ryuichi and Matsui, Ko},
  issn         = {08966273},
  journal      = {Neuron},
  number       = {2},
  pages        = {314 -- 320},
  publisher    = {Elsevier},
  title        = {{Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage}},
  doi          = {10.1016/j.neuron.2013.11.011},
  volume       = {81},
  year         = {2014},
}

@article{2242,
  abstract     = {MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct influence of miR-155 on the expression levels of other miRNAs. For example, miR-455 is negatively regulated in miR-155-deficient cells possibly due to inhibition of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data sets, we propose a model of hierarchical miRNA expression dominated by miR-155 in DCs and macrophages.},
  author       = {Dueck, Anne and Eichner, Alexander and Sixt, Michael K and Meister, Gunter},
  issn         = {00145793},
  journal      = {FEBS Letters},
  number       = {4},
  pages        = {632 -- 640},
  publisher    = {Elsevier},
  title        = {{A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation}},
  doi          = {10.1016/j.febslet.2014.01.009},
  volume       = {588},
  year         = {2014},
}

@inbook{2245,
  abstract     = {Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application. },
  author       = {Simon, Sibu and Skůpa, Petr and Dobrev, Petre and Petrášek, Jan and Zažímalová, Eva and Friml, Jirí},
  booktitle    = {Plant Chemical Genomics},
  editor       = {Hicks, Glenn and Robert, Stéphanie},
  issn         = {10643745},
  pages        = {255 -- 264},
  publisher    = {Springer},
  title        = {{Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters}},
  doi          = {10.1007/978-1-62703-592-7_23},
  volume       = {1056},
  year         = {2014},
}

@article{2246,
  abstract     = {Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth. },
  author       = {Grinshpun, Andrey and Phalitnonkiat, Pakawat and Rubin, Sasha and Tarfulea, Andrei},
  issn         = {03043975},
  journal      = {Theoretical Computer Science},
  pages        = {73 -- 91},
  publisher    = {Elsevier},
  title        = {{Alternating traps in Muller and parity games}},
  doi          = {10.1016/j.tcs.2013.11.032},
  volume       = {521},
  year         = {2014},
}

@article{2248,
  abstract     = {Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain.},
  author       = {Capek, Daniel and Metscher, Brian and Müller, Gerd},
  issn         = {15525007},
  journal      = {Journal of Experimental Zoology Part B: Molecular and Developmental Evolution},
  number       = {1},
  pages        = {1 -- 12},
  publisher    = {Wiley-Blackwell},
  title        = {{Thumbs down: A molecular-morphogenetic approach to avian digit homology}},
  doi          = {10.1002/jez.b.22545},
  volume       = {322},
  year         = {2014},
}

@article{2249,
  abstract     = {The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes.},
  author       = {Chen, Yani and Aung, Kyaw and Rolčík, Jakub and Walicki, Kathryn and Friml, Jirí and Brandizzí, Federica},
  issn         = {09607412},
  journal      = {Plant Journal},
  number       = {1},
  pages        = {97 -- 107},
  publisher    = {Wiley-Blackwell},
  title        = {{Inter-regulation of the unfolded protein response and auxin signaling}},
  doi          = {10.1111/tpj.12373},
  volume       = {77},
  year         = {2014},
}

@article{2250,
  abstract     = {The genome sequences of new viruses often contain many "orphan" or "taxon-specific" proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as "genus specific" by BLAST. More powerful methods developed recently, such as HHblits or HHpred (available through web-based, user-friendly interfaces), could detect distant homologs of a quarter of these proteins, suggesting that these methods should be used to annotate viral genomes. In-depth manual analyses of a subset of the remaining sequences, guided by contextual information such as taxonomy, gene order, or domain cooccurrence, identified distant homologs of another third. Thus, a combination of powerful automated methods and manual analyses can uncover distant homologs of many proteins thought to be orphans. We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses. As an application, we reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We could identify homologs of most of its proteins thought to be orphans; in each case, identifying homologs provided functional clues. We discovered that CBPV encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase; a putative membrane protein, SP24, with homologs in unrelated insect viruses and insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses, blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found in negeviruses. SP24 and ORF2 are probably major structural components of the virionsd.},
  author       = {Kuchibhatla, Durga and Sherman, Westley and Chung, Betty and Cook, Shelley and Schneider, Georg and Eisenhaber, Birgit and Karlin, David},
  issn         = {0022538X},
  journal      = {Journal of Virology},
  number       = {1},
  pages        = {10 -- 20},
  publisher    = {ASM},
  title        = {{Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins}},
  doi          = {10.1128/JVI.02595-13},
  volume       = {88},
  year         = {2014},
}