@article{12193,
  abstract     = {DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.},
  author       = {Walker, James and Gao, Hongbo and Zhang, Jingyi and Aldridge, Billy and Vickers, Martin and Higgins, James D. and Feng, Xiaoqi},
  issn         = {1546-1718},
  journal      = {Nature Genetics},
  keywords     = {Genetics},
  number       = {1},
  pages        = {130--137},
  publisher    = {Nature Research},
  title        = {{Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis}},
  doi          = {10.1038/s41588-017-0008-5},
  volume       = {50},
  year         = {2017},
}

@article{1228,
  abstract     = {Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.},
  author       = {Sauerzopf, Ulrich and Sacco, Roberto and Novarino, Gaia and Niello, Marco and Weidenauer, Ana and Praschak Rieder, Nicole and Sitte, Harald and Willeit, Matthaeus},
  journal      = {European Journal of Neuroscience},
  number       = {1},
  pages        = {45 -- 57},
  publisher    = {Wiley-Blackwell},
  title        = {{Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence}},
  doi          = {10.1111/ejn.13418},
  volume       = {45},
  year         = {2017},
}

@article{123,
  abstract     = {The Leidenfrost effect occurs when an object near a hot surface vaporizes rapidly enough to lift itself up and hover. Although well understood for liquids and stiff sublimable solids, nothing is known about the effect with materials whose stiffness lies between these extremes. Here we introduce a new phenomenon that occurs with vaporizable soft solids - the elastic Leidenfrost effect. By dropping hydrogel spheres onto hot surfaces we find that, rather than hovering, they energetically bounce several times their diameter for minutes at a time. With high-speed video during a single impact, we uncover high-frequency microscopic gap dynamics at the sphere/substrate interface. We show how these otherwise-hidden agitations constitute work cycles that harvest mechanical energy from the vapour and sustain the bouncing. Our findings suggest a new strategy for injecting mechanical energy into a widely used class of soft materials, with potential relevance to fields such as active matter, soft robotics and microfluidics.},
  author       = {Waitukaitis, Scott R and Zuiderwijk, Antal and Souslov, Anton and Coulais, Corentin and Van Hecke, Martin},
  journal      = {Nature Physics},
  number       = {11},
  pages        = {1095 -- 1099},
  publisher    = {Nature Publishing Group},
  title        = {{Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing}},
  doi          = {10.1038/nphys4194},
  volume       = {13},
  year         = {2017},
}

@inproceedings{12571,
  abstract     = {We consider the problems of maintaining approximate maximum matching and minimum vertex cover in a dynamic graph. Starting with the seminal work of Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. Very recently, extending the framework of Baswana, Gupta and Sen [FOCS 2011], Solomon [FOCS 2016] gave a randomized 2-approximation dynamic algorithm for this problem that has amortized update time of O(1) with high probability. We consider the natural open question of derandomizing this result. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya, Henzinger and Italiano [SODA 2015]; it had an approximation ratio of (2+ϵ) and an amortized update time of O(logn/ϵ2). Our result can be generalized to give a fully dynamic O(f3)-approximation algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional matching problems, where every hyperedge has at most f vertices.},
  author       = {Bhattacharya, Sayan and Chakrabarty, Deeparnab and Henzinger, Monika H},
  booktitle    = {19th International Conference on Integer Programming and Combinatorial Optimization},
  isbn         = {9783319592497},
  issn         = {0302-9743},
  location     = {Waterloo, ON, Canada},
  pages        = {86--98},
  publisher    = {Springer Nature},
  title        = {{Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time}},
  doi          = {10.1007/978-3-319-59250-3_8},
  volume       = {10328},
  year         = {2017},
}

@article{12608,
  abstract     = {The spatio-temporal distribution of air temperature over mountain glaciers can demonstrate complex patterns, yet it is often represented simplistically using linear vertical temperature gradients (VTGs) extrapolated from off-glacier locations. We analyse a network of centreline and lateral air temperature observations at Tsanteleina Glacier, Italy, during summer 2015. On average, VTGs are steep (&lt;−0.0065 °C m<jats:sup>−1</jats:sup>), but they are shallow under warm ambient conditions when the correlation between air temperature and elevation becomes weaker. Published along-flowline temperature distribution methods explain centreline observations well, including warming on the lower glacier tongue, but cannot estimate lateral temperature variability. Application of temperature distribution methods improves simulation of melt rates (RMSE) in an energy-balance model by up to 36% compared to the environmental lapse rate extrapolated from an off-glacier station. However, results suggest that model parameters are not easily transferable to glaciers with a small fetch without recalibration. Such methods have potential to improve estimates of temperature across a glacier, but their parameter transferability should be further linked to the glacier and atmospheric characteristics. Furthermore, ‘cold spots’, which can be &gt;2°C cooler than expected for their elevation, whose occurrence is not predicted by the temperature distribution models, are identified at one-quarter of the measurement sites.},
  author       = {SHAW, THOMAS E. and BROCK, BEN W. and AYALA, ÁLVARO and RUTTER, NICK and Pellicciotti, Francesca},
  issn         = {1727-5652},
  journal      = {Journal of Glaciology},
  keywords     = {Earth-Surface Processes},
  number       = {242},
  pages        = {973--988},
  publisher    = {Cambridge University Press},
  title        = {{Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations}},
  doi          = {10.1017/jog.2017.65},
  volume       = {63},
  year         = {2017},
}

@article{12609,
  abstract     = {Previous estimates of melt and surface sublimation on glaciers of the subtropical semiarid Andes (29–34°S) have been obtained at few specific locations, but it is not clear how ablation components vary across the entire extent of a glacier in this dry environment. Here, we simulate the distributed energy and mass balance of Juncal Norte Glacier (33°S) during a 2-month summer period. Forcing fields of near-surface air temperature and wind speed are generated using two methods accounting for the main physical processes that shape their spatial variations. Simulated meteorological variables and ablation agree well with observations on the glacier tongue and reveal complex patterns of energy and mass fluxes. Ablation decreases from 70 mm w.e. d<jats:sup>−1</jats:sup> at the low-albedo glacier terminus (~3000 m), where almost 100% of total ablation corresponds to melt, to &lt;5 mm w.e. d<jats:sup>−1</jats:sup> at wind-exposed, strong-radiated sites above 5500 m, where surface sublimation represents &gt;75% of total ablation. Our simulations provide the first glacier-scale estimates of ablation components on a glacier in the study region and better reproduce the observed and expected spatial variations of melt and surface sublimation, in comparison with more simple assumptions, such as linear gradients and uniform wind speeds.},
  author       = {AYALA, A. and Pellicciotti, Francesca and PELEG, N. and BURLANDO, P.},
  issn         = {1727-5652},
  journal      = {Journal of Glaciology},
  keywords     = {Earth-Surface Processes},
  number       = {241},
  pages        = {803--822},
  publisher    = {Cambridge University Press},
  title        = {{Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile}},
  doi          = {10.1017/jog.2017.46},
  volume       = {63},
  year         = {2017},
}

@article{12610,
  abstract     = {The hydrological systems of heavily-downwasted debris-covered glaciers differ from those of clean-ice glaciers due to the hummocky surface and debris mantle of such glaciers, leading to a relatively limited understanding of drainage pathways. Supraglacial ponds represent sinks within the discontinuous supraglacial drainage system, and occasionally drain englacially. To assess pond dynamics, we made pond water level measurements on Lirung Glacier, Nepal, during May and October of 2013 and 2014. Simultaneously, aerial, satellite, and terrestrial orthoimages and digital elevation models were obtained, providing snapshots of the ponds and their surroundings. We performed a DEM-based analysis of the glacier's closed surface catchments to identify surface drainage pathways and englacial drainage points, and compared this to field observations of surface and near-surface water flow. The total ponded area was higher in the pre-monsoon than post-monsoon, with individual ponds filling and draining seasonally associated with the surface exposure of englacial conduit segments. We recorded four pond drainage events, all of which occurred gradually (duration of weeks), observed diurnal fluctuations indicative of varying water supply and outflow discharge, and we documented instances of interaction between distant ponds. The DEM drainage analysis identified numerous sinks >3 m in depth across the glacier surface, few of which exhibited ponds (23%), while the field survey highlighted instances of surface water only explicable via englacial routes. Taken together, our observations provide evidence for widespread supraglacial-englacial connectivity of meltwater drainage paths. Results suggest that successive englacial conduit collapse events, themselves likely driven by supraglacial pond drainage, cause the glacier surface drainage system to evolve into a configuration following relict englacial conduit systems. Within this system, ponds form in depressions of reduced drainage efficiency and link the supraglacial and englacial drainage networks.},
  author       = {Miles, Evan S. and Steiner, Jakob and Willis, Ian and Buri, Pascal and Immerzeel, Walter W. and Chesnokova, Anna and Pellicciotti, Francesca},
  issn         = {2296-6463},
  journal      = {Frontiers in Earth Science},
  keywords     = {General Earth and Planetary Sciences},
  publisher    = {Frontiers Media},
  title        = {{Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal}},
  doi          = {10.3389/feart.2017.00069},
  volume       = {5},
  year         = {2017},
}

@article{12611,
  abstract     = {We investigate the energy balance and ablation regimes of glaciers in high-elevation, dry environments using glaciometeorological data collected on six glaciers in the semiarid Andes of North-Central Chile (29–34°S, 3127–5324 m). We use a point-scale physically based energy balance (EB) model and an enhanced Temperature-Index (ETI) model that calculates melt rates only as a function of air temperature and net shortwave radiation. At all sites, the largest energy inputs are net shortwave and incoming longwave radiation, which are controlled by surface albedo and elevation, respectively. Turbulent fluxes cancel each other out at the lower sites, but as elevation increases, cold, dry and wind-exposed conditions increase the magnitude of negative latent heat fluxes, associated with large surface sublimation rates. In midsummer (January), ablation rates vary from 67.9 mm w.e. d−1 at the lowest site (∼100% corresponding to melt), to 2.3 mm w.e. d−1 at the highest site (>85% corresponding to surface sublimation). At low-elevation, low-albedo, melt-dominated sites, the ETI model correctly reproduces melt using a large range of possible parameters, but both the performance and parameter transferability decrease with elevation for two main reasons: (i) the air temperature threshold approach for melt onset does not capture the diurnal variability of melt in cold and strong irradiated environments and (ii) energy losses decrease the correlation between melt and net shortwave radiation. We summarize our results by means of an elevation profile of ablation components that can be used as reference in future studies of glacier ablation in the semiarid Andes.},
  author       = {Ayala, A. and Pellicciotti, Francesca and MacDonell, S. and McPhee, J. and Burlando, P.},
  issn         = {0043-1397},
  journal      = {Water Resources Research},
  keywords     = {Water Science and Technology},
  number       = {7},
  pages        = {5601--5625},
  publisher    = {American Geophysical Union},
  title        = {{Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions}},
  doi          = {10.1002/2016wr020126},
  volume       = {53},
  year         = {2017},
}

@article{12612,
  abstract     = {Supraglacial ponds play a key role in absorbing atmospheric energy and directing it to the ice of debris-covered glaciers, but the spatial and temporal distribution of these features is not well documented. We analyse 172 Landsat TM/ETM+ scenes for the period 1999–2013 to identify thawed supraglacial ponds for the debris-covered tongues of five glaciers in the Langtang Valley of Nepal. We apply an advanced atmospheric correction routine (Landcor/6S) and use band ratio and image morphological techniques to identify ponds and validate our results with 2.5 m Cartosat-1 observations. We then characterize the spatial, seasonal and interannual patterns of ponds. We find high variability in pond incidence between glaciers (May–October means of 0.08–1.69% of debris area), with ponds most frequent in zones of low surface gradient and velocity. The ponds show pronounced seasonality, appearing in the pre-monsoon as snow melts, peaking at the monsoon onset at 2% of debris-covered area, then declining in the post-monsoon as ponds drain or freeze. Ponds are highly recurrent and persistent, with 40.5% of pond locations occurring for multiple years. Rather than a trend in pond cover over the study period, we find high interannual variability for each glacier after controlling for seasonality.},
  author       = {MILES, EVAN S. and WILLIS, IAN C. and ARNOLD, NEIL S. and STEINER, JAKOB and Pellicciotti, Francesca},
  issn         = {1727-5652},
  journal      = {Journal of Glaciology},
  keywords     = {Earth-Surface Processes},
  number       = {237},
  pages        = {88--105},
  publisher    = {Cambridge University Press},
  title        = {{Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013}},
  doi          = {10.1017/jog.2016.120},
  volume       = {63},
  year         = {2017},
}

@inproceedings{12905,
  author       = {Schlögl, Alois and Kiss, Janos},
  booktitle    = {AHPC17 – Austrian HPC Meeting 2017},
  location     = {Grundlsee, Austria},
  pages        = {28},
  publisher    = {FSP Scientific Computing},
  title        = {{Scientific Computing at IST Austria}},
  year         = {2017},
}

@article{1294,
  abstract     = {We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints.},
  author       = {Brázdil, Tomáš and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín},
  journal      = {Journal of Computer and System Sciences},
  pages        = {144 -- 170},
  publisher    = {Elsevier},
  title        = {{Trading performance for stability in Markov decision processes}},
  doi          = {10.1016/j.jcss.2016.09.009},
  volume       = {84},
  year         = {2017},
}

@inproceedings{13160,
  abstract     = {Transforming deterministic ω
-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae.},
  author       = {Kretinsky, Jan and Meggendorfer, Tobias and Waldmann, Clara and Weininger, Maximilian},
  booktitle    = {Tools and Algorithms for the Construction and Analysis of Systems},
  isbn         = {9783662545768},
  issn         = {1611-3349},
  location     = {Uppsala, Sweden},
  pages        = {443--460},
  publisher    = {Springer},
  title        = {{Index appearance record for transforming Rabin automata into parity automata}},
  doi          = {10.1007/978-3-662-54577-5_26},
  volume       = {10205},
  year         = {2017},
}

@phdthesis{820,
  abstract     = {The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.
In Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.
In Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.
To start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.},
  author       = {Jesse, Fabienne},
  issn         = {2663-337X},
  pages        = {87},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The lac operon in the wild}},
  doi          = {10.15479/AT:ISTA:th_857},
  year         = {2017},
}

@phdthesis{821,
  abstract     = {This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the
static analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.
Our contributions can be broadly grouped into five categories.

Our first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.
It has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.
We utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.
In most cases we make an algebraic treatment of the considered problem,
where several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. 
We exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, 
and provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.
We also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,
namely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.


Our second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.
In particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.
Additionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,
where the task is to obtain analysis summaries of library code in the presence of callbacks.
Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.
Finally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.
This hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.


Our third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.
In this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures
the magnitude of their respective effect.
The Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.
We illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,
and present some case studies to this direction.


Our fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between  traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.
We present a new dynamic partial-order reduction method  called the Data-centric Partial Order Reduction (DC-DPOR).
Our algorithm is based on a new equivalence between traces, called the observation equivalence.
DC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.
Depending on the program, the new partitioning can be even exponentially coarser.
Additionally, DC-DPOR spends only polynomial time in each explored class.


Our fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.
On the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.
On the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show
how the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games.},
  author       = {Pavlogiannis, Andreas},
  issn         = {2663-337X},
  pages        = {418},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Algorithmic advances in program analysis and their applications}},
  doi          = {10.15479/AT:ISTA:th_854},
  year         = {2017},
}

@article{822,
  abstract     = {Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. },
  author       = {De Vos, Marjon and Zagórski, Marcin P and Mcnally, Alan and Bollenbach, Mark Tobias},
  issn         = {00278424},
  journal      = {PNAS},
  number       = {40},
  pages        = {10666 -- 10671},
  publisher    = {National Academy of Sciences},
  title        = {{Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections}},
  doi          = {10.1073/pnas.1713372114},
  volume       = {114},
  year         = {2017},
}

@article{823,
  abstract     = {The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.},
  author       = {Colabrese, Simona and De Martino, Daniele and Leuzzi, Luca and Marinari, Enzo},
  issn         = {17425468},
  journal      = { Journal of Statistical Mechanics: Theory and Experiment},
  number       = {9},
  publisher    = {IOPscience},
  title        = {{Phase transitions in integer linear problems}},
  doi          = {10.1088/1742-5468/aa85c3},
  volume       = {2017},
  year         = {2017},
}

@article{8235,
  abstract     = {Due to large homology of human and canine EGFR, dogs suffering from spontaneous EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic compounds can be developed for both human and veterinary patients. This study describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc. Successful coupling of 10 DTPA molecules per antibody on average was proven by significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots. Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained its binding capacity towards human and canine EGFR in flow cytometry, immuno- and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma cells by a competition binding technique. Stability tests of the radiolabeled compound identified TRIS buffered saline as the ideal formulation for short-term storage with 87.11 ±6.04% intact compound being still detected 60 minutes post radiolabeling. High stability, specificity and EGFR binding affinity pinpoint towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the first proof-of-concept diagnostic and therapeutic applications in canine cancer patients.},
  author       = {Fazekas-Singer, Judit and Berroterán-Infante, Neydher and Rami-Mark, Christina and Dumanic, Monika and Matz, Miroslawa and Willmann, Michael and Andreae, Fritz and Singer, Josef and Wadsak, Wolfgang and Mitterhauser, Markus and Jensen-Jarolim, Erika},
  issn         = {1949-2553},
  journal      = {Oncotarget},
  pages        = {83128--83141},
  publisher    = {Impact Journals},
  title        = {{Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials}},
  doi          = {10.18632/oncotarget.20914},
  volume       = {8},
  year         = {2017},
}

@article{8236,
  abstract     = {Th2 immunity and allergic immune surveillance play critical roles in host responses to pathogens, parasites and allergens. Numerous studies have reported significant links between Th2 responses and cancer, including insights into the functions of IgE antibodies and associated effector cells in both antitumour immune surveillance and therapy. The interdisciplinary field of AllergoOncology was given Task Force status by the European Academy of Allergy and Clinical Immunology in 2014. Affiliated expert groups focus on the interface between allergic responses and cancer, applied to immune surveillance, immunomodulation and the functions of IgE‐mediated immune responses against cancer, to derive novel insights into more effective treatments. Coincident with rapid expansion in clinical application of cancer immunotherapies, here we review the current state‐of‐the‐art and future translational opportunities, as well as challenges in this relatively new field. Recent developments include improved understanding of Th2 antibodies, intratumoral innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation by dendritic cells, as well as immunotherapeutic strategies such as vaccines and recombinant antibodies, and finally, the management of allergy in daily clinical oncology. Shedding light on the crosstalk between allergic response and cancer is paving the way for new avenues of treatment.},
  author       = {Jensen-Jarolim, E. and Bax, H. J. and Bianchini, R. and Capron, M. and Corrigan, C. and Castells, M. and Dombrowicz, D. and Daniels-Wells, T. R. and Fazekas, Judit and Fiebiger, E. and Gatault, S. and Gould, H. J. and Janda, J. and Josephs, D. H. and Karagiannis, P. and Levi-Schaffer, F. and Meshcheryakova, A. and Mechtcheriakova, D. and Mekori, Y. and Mungenast, F. and Nigro, E. A. and Penichet, M. L. and Redegeld, F. and Saul, L. and Singer, J. and Spicer, J. F. and Siccardi, A. G. and Spillner, E. and Turner, M. C. and Untersmayr, E. and Vangelista, L. and Karagiannis, S. N.},
  issn         = {0105-4538},
  journal      = {Allergy},
  number       = {6},
  pages        = {866--887},
  publisher    = {Wiley},
  title        = {{AllergoOncology - the impact of allergy in oncology: EAACI position paper}},
  doi          = {10.1111/all.13119},
  volume       = {72},
  year         = {2017},
}

@article{8237,
  abstract     = {Monoclonal antibodies find broad application as therapy for various types of cancer by employing multiple mechanisms of action against tumors. Manipulating the Fc-mediated functions of antibodies that engage immune effector cells, such as NK cells, represents a strategy to influence effector cell activation and to enhance antibody potency and potentially efficacy. We developed a novel approach to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies. This entailed coupling single expression vector (pVitro1) antibody cloning, using polymerase incomplete primer extension (PIPE) polymerase chain reaction, together with simultaneous Fc region point mutagenesis and high yield transient expression in human mammalian cells. Employing this, we engineered wild type, low (N297Q, NQ), and high (S239D/I332E, DE) FcR-binding Fc mutant monoclonal antibody panels recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan 4. Antibodies were generated with universal mutagenic primers applicable to any IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in small culture volumes, at high yields and within 12 days from design to purified material. Antibody variants conserved their Fab-mediated recognition of target antigens and their direct anti-proliferative effects against cancer cells. Fc mutations had a significant impact on antibody interactions with Fc receptors (FcRs) on human NK cells, and consequently on the potency of NK cell activation, quantified by immune complex-mediated calcium mobilization and by antibody-dependent cellular cytotoxicity (ADCC) of tumor cells. This strategy for manipulation and testing of Fc region engagement with cognate FcRs can facilitate the design of antibodies with defined effector functions and potentially enhanced efficacy against tumor cells.},
  author       = {Ilieva, Kristina M. and Fazekas-Singer, Judit and Achkova, Daniela Y. and Dodev, Tihomir S. and Mele, Silvia and Crescioli, Silvia and Bax, Heather J. and Cheung, Anthony and Karagiannis, Panagiotis and Correa, Isabel and Figini, Mariangela and Marlow, Rebecca and Josephs, Debra H. and Beavil, Andrew J. and Maher, John and Spicer, James F. and Jensen-Jarolim, Erika and Tutt, Andrew N. and Karagiannis, Sophia N.},
  issn         = {1664-3224},
  journal      = {Frontiers in Immunology},
  publisher    = {Frontiers},
  title        = {{Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields}},
  doi          = {10.3389/fimmu.2017.01112},
  volume       = {8},
  year         = {2017},
}

@article{8239,
  abstract     = {Acrolein, a highly reactive unsaturated aldehyde, is generated in large amounts during smoking and is best known for its genotoxic capacity. Here, we aimed to assess whether acrolein at concentrations relevant for smokers may also exert immunomodulatory effects that could be relevant in allergy or cancer. In a BALB/c allergy model repeated nasal exposure to acrolein abrogated allergen-specific antibody and cytokine formation, and led to a relative accumulation of regulatory T cells in the lungs. Only the acrolein-treated mice were protected from bronchial hyperreactivity as well as from anaphylactic reactions upon challenge with the specific allergen. Moreover, grafted D2F2 tumor cells grew faster and intratumoral Foxp3+ cell accumulation was observed in these mice compared to sham-treated controls. Results from reporter cell lines suggested that acrolein acts via the aryl-hydrocarbon receptor which could be inhibited by resveratrol and 3′-methoxy-4′-nitroflavone Acrolein- stimulation of human PBMCs increased Foxp3+ expression by T cells which could be antagonized by resveratrol. Our mouse and human data thus revealed that acrolein exerts systemic immunosuppression by promoting Foxp3+ regulatory cells. This provides a novel explanation why smokers have a lower allergy, but higher cancer risk.},
  author       = {Roth-Walter, Franziska and Bergmayr, Cornelia and Meitz, Sarah and Buchleitner, Stefan and Stremnitzer, Caroline and Fazekas, Judit and Moskovskich, Anna and Müller, Mario A. and Roth, Georg A. and Manzano-Szalai, Krisztina and Dvorak, Zdenek and Neunkirchner, Alina and Jensen-Jarolim, Erika},
  issn         = {2045-2322},
  journal      = {Scientific Reports},
  publisher    = {Springer Nature},
  title        = {{Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure}},
  doi          = {10.1038/srep45067},
  volume       = {7},
  year         = {2017},
}