@article{6504,
abstract = {Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.
Here, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.
Moreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.
Our results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response.},
author = {Zhang, Yuzhou and He, P and Ma, X and Yang, Z and Pang, C and Yu, J and Wang, G and Friml, Jiří and Xiao, G},
issn = {0028-646x},
journal = {New Phytologist},
publisher = {Wiley},
title = {{Auxin-mediated statolith production for root gravitropism}},
doi = {10.1111/nph.15932},
year = {2019},
}
@article{6511,
abstract = {Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N).},
author = {Bao, Zhigang and Erdös, László and Schnelli, Kevin},
issn = {00911798},
journal = {Annals of Probability},
number = {3},
pages = {1270--1334},
publisher = {Project Euclid},
title = {{Local single ring theorem on optimal scale}},
doi = {10.1214/18-AOP1284},
volume = {47},
year = {2019},
}
@article{6559,
abstract = {Branching morphogenesis is a prototypical example of complex three-dimensional organ sculpting, required in multiple developmental settings to maximize the area of exchange surfaces. It requires, in particular, the coordinated growth of different cell types together with complex patterning to lead to robust macroscopic outputs. In recent years, novel multiscale quantitative biology approaches, together with biophysical modelling, have begun to shed new light of this topic. Here, we wish to review some of these recent developments, highlighting the generic design principles that can be abstracted across different branched organs, as well as the implications for the broader fields of stem cell, developmental and systems biology.},
author = {Hannezo, Edouard B and Simons, Benjamin D.},
issn = {18790410},
journal = {Current Opinion in Cell Biology},
pages = {99--105},
publisher = {Elsevier},
title = {{Multiscale dynamics of branching morphogenesis}},
doi = {10.1016/j.ceb.2019.04.008},
volume = {60},
year = {2019},
}
@article{6566,
abstract = {Methodologies that involve the use of nanoparticles as “artificial atoms” to rationally build materials in a bottom-up fashion are particularly well-suited to control the matter at the nanoscale. Colloidal synthetic routes allow for an exquisite control over such “artificial atoms” in terms of size, shape, and crystal phase as well as core and surface compositions. We present here a bottom-up approach to produce Pb–Ag–K–S–Te nanocomposites, which is a highly promising system for thermoelectric energy conversion. First, we developed a high-yield and scalable colloidal synthesis route to uniform lead sulfide (PbS) nanorods, whose tips are made of silver sulfide (Ag2S). We then took advantage of the large surface-to-volume ratio to introduce a p-type dopant (K) by replacing native organic ligands with K2Te. Upon thermal consolidation, K2Te-surface modified PbS–Ag2S nanorods yield p-type doped nanocomposites with PbTe and PbS as major phases and Ag2S and Ag2Te as embedded nanoinclusions. Thermoelectric characterization of such consolidated nanosolids showed a high thermoelectric figure-of-merit of 1 at 620 K.},
author = {Ibáñez, Maria and Genç, Aziz and Hasler, Roger and Liu, Yu and Dobrozhan, Oleksandr and Nazarenko, Olga and Mata, María de la and Arbiol, Jordi and Cabot, Andreu and Kovalenko, Maksym V.},
issn = {1936-086X},
journal = {ACS Nano},
keyword = {colloidal nanoparticles, asymmetric nanoparticles, inorganic ligands, heterostructures, catalyst assisted growth, nanocomposites, thermoelectrics},
number = {6},
pages = {6572--6580},
publisher = {ACS},
title = {{Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks}},
doi = {10.1021/acsnano.9b00346},
volume = {13},
year = {2019},
}
@article{6617,
abstract = {The effective large-scale properties of materials with random heterogeneities on a small scale are typically determined by the method of representative volumes: a sample of the random material is chosen—the representative volume—and its effective properties are computed by the cell formula. Intuitively, for a fixed sample size it should be possible to increase the accuracy of the method by choosing a material sample which captures the statistical properties of the material particularly well; for example, for a composite material consisting of two constituents, one would select a representative volume in which the volume fraction of the constituents matches closely with their volume fraction in the overall material. Inspired by similar attempts in materials science, Le Bris, Legoll and Minvielle have designed a selection approach for representative volumes which performs remarkably well in numerical examples of linear materials with moderate contrast. In the present work, we provide a rigorous analysis of this selection approach for representative volumes in the context of stochastic homogenization of linear elliptic equations. In particular, we prove that the method essentially never performs worse than a random selection of the material sample and may perform much better if the selection criterion for the material samples is chosen suitably.},
author = {Fischer, Julian L},
journal = {Archive for Rational Mechanics and Analysis},
publisher = {Springer},
title = {{The choice of representative volumes in the approximation of effective properties of random materials}},
doi = {10.1007/s00205-019-01400-w},
year = {2019},
}
@article{6631,
abstract = {The spatiotemporal organization of cell divisions constitutes an integral part in the development of multicellular organisms, and mis-regulation of cell divisions can lead to severe developmental defects. Cell divisions have an important morphogenetic function in development by regulating growth and shape acquisition of developing tissues, and, conversely, tissue morphogenesis is known to affect both the rate and orientation of cell divisions. Moreover, cell divisions are associated with an extensive reorganization of the cytoskeleton and adhesion apparatus in the dividing cells that in turn can affect large-scale tissue rheological properties. Thus, the interplay between cell divisions and tissue morphogenesis plays a key role in embryo and tissue morphogenesis.},
author = {Godard, Benoit G and Heisenberg, Carl-Philipp J},
journal = {Current Opinion in Cell Biology},
pages = {114--120},
publisher = {Elsevier},
title = {{Cell division and tissue mechanics}},
doi = {10.1016/j.ceb.2019.05.007},
volume = {60},
year = {2019},
}
@inproceedings{6648,
abstract = {Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory
needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.},
author = {Edelsbrunner, Herbert and Virk, Ziga and Wagner, Hubert},
booktitle = {35th International Symposium on Computational Geometry},
isbn = {9783959771047},
location = {Portland, OR, United States},
pages = {31:1--31:14},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Topological data analysis in information space}},
doi = {10.4230/LIPICS.SOCG.2019.31},
volume = {129},
year = {2019},
}
@article{6477,
abstract = {Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions.},
author = {Abanin, Dmitry A. and Altman, Ehud and Bloch, Immanuel and Serbyn, Maksym},
issn = {0034-6861},
journal = {Reviews of Modern Physics},
number = {2},
publisher = {APS Physics},
title = {{Colloquium: Many-body localization, thermalization, and entanglement}},
doi = {10.1103/revmodphys.91.021001},
volume = {91},
year = {2019},
}
@article{6650,
abstract = {We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry.},
author = {Alderighi, Thomas and Malomo, Luigi and Giorgi, Daniela and Bickel, Bernd and Cignoni, Paolo and Pietroni, Nico},
issn = {0730-0301},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Volume-aware design of composite molds}},
doi = {10.1145/3306346.3322981},
volume = {38},
year = {2019},
}
@article{6713,
abstract = {Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.},
author = {Castro, João Pl and Yancoskie, Michelle N. and Marchini, Marta and Belohlavy, Stefanie and Hiramatsu, Layla and Kučka, Marek and Beluch, William H. and Naumann, Ronald and Skuplik, Isabella and Cobb, John and Barton, Nicholas H and Rolian, Campbell and Chan, Yingguang Frank},
journal = {eLife},
publisher = {eLife},
title = {{An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice}},
doi = {10.7554/eLife.42014},
volume = {8},
year = {2019},
}
@inproceedings{6725,
abstract = {A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language.
Recent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds.},
author = {Kolmogorov, Vladimir},
booktitle = {46th International Colloquium on Automata, Languages and Programming},
isbn = {978-3-95977-109-2},
issn = {1868-8969},
location = {Patras, Greece},
pages = {77:1--77:12},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Testing the complexity of a valued CSP language}},
doi = {10.4230/LIPICS.ICALP.2019.77},
volume = {132},
year = {2019},
}
@article{6756,
abstract = {We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over 𝕊2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.},
author = {Pranav, Pratyush and Adler, Robert J. and Buchert, Thomas and Edelsbrunner, Herbert and Jones, Bernard J.T. and Schwartzman, Armin and Wagner, Hubert and Van De Weygaert, Rien},
issn = {14320746},
journal = {Astronomy and Astrophysics},
publisher = {EDP Sciences},
title = {{Unexpected topology of the temperature fluctuations in the cosmic microwave background}},
doi = {10.1051/0004-6361/201834916},
volume = {627},
year = {2019},
}
@phdthesis{6371,
abstract = {Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation.
i) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model.
ii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites.
iii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background.
iv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter.
We demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation.
},
author = {Igler, Claudia},
issn = {2663-337X},
keyword = {gene regulation, biophysics, transcription factor binding, bacteria},
pages = {152},
publisher = {IST Austria},
title = {{On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation}},
doi = {10.15479/AT:ISTA:6371},
year = {2019},
}
@article{6821,
abstract = {To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined.},
author = {Yourick, Miranda R. and Sandkam, Benjamin A. and Gammerdinger, William J and Escobar-Camacho, Daniel and Nandamuri, Sri Pratima and Clark, Frances E. and Joyce, Brendan and Conte, Matthew A. and Kocher, Thomas D. and Carleton, Karen L.},
journal = {Molecular Ecology Resources},
publisher = {Wiley},
title = {{Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses}},
doi = {10.1111/1755-0998.13062},
year = {2019},
}
@article{6763,
abstract = {When grape-sized aqueous dimers are irradiated in a microwave oven, an intense electromagnetic hotspot forms at their point of contact, often igniting a plasma. Here we show that this irradiation can result in the injection of mechanical energy. By examining irradiated hydrogel dimers through high-speed imaging, we find that they repeatedly bounce off of each other while irradiated. We determine that an average of 1 lJ of mechanical energy is injected into the pair during each collision. Furthermore, a characteristic high-pitched audio signal is found to accompany each collision.
We show that both the audio signal and the energy injection arise via an interplay between vaporization and elastic deformations in the region of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish a novel, non-contact method of injecting mechanical energy into soft matter systems, suggesting application in fields such as soft robotics.},
author = {Khattak, Hamza K. and Waitukaitis, Scott R and Slepkov, Aaron D.},
issn = {17446848},
journal = {Soft Matter},
number = {29},
pages = {5804--5809},
publisher = {Royal Society of Chemistry},
title = {{Microwave induced mechanical activation of hydrogel dimers}},
doi = {10.1039/c9sm00756c},
volume = {15},
year = {2019},
}
@article{6857,
abstract = {Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.
The recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.},
author = {Giese, B and Friess, J L and Schetelig, M F and Barton, Nicholas H and Messer, Philip and Debarre, Florence and Meimberg, H and Windbichler, N and Boete, C},
journal = {BioEssays},
publisher = {Wiley},
title = {{Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna}},
doi = {10.1002/bies.201900151},
year = {2019},
}
@article{5986,
abstract = {Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm (with 𝑂(𝑛8) being a crude bound on the run-time) to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of 𝑂(𝑛7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.},
author = {Lubiw, Anna and Masárová, Zuzana and Wagner, Uli},
issn = {0179-5376},
journal = {Discrete & Computational Geometry},
number = {4},
pages = {880--898},
publisher = {Springer Nature},
title = {{A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations}},
doi = {10.1007/s00454-018-0035-8},
volume = {61},
year = {2019},
}
@phdthesis{6681,
abstract = {The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.
However, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,
we construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).
In the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space.},
author = {Zhechev, Stephan Y},
issn = {2663-337X},
pages = {104},
publisher = {IST Austria},
title = {{Algorithmic aspects of homotopy theory and embeddability}},
doi = {10.15479/AT:ISTA:6681},
year = {2019},
}
@article{6819,
abstract = {Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.},
author = {Antoniou, Michael N. and Nicolas, Armel and Mesnage, Robin and Biserni, Martina and Rao, Francesco V. and Martin, Cristina Vazquez},
issn = {1756-0500},
journal = {BMC Research Notes},
publisher = {Springer Nature},
title = {{Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells}},
doi = {10.1186/s13104-019-4534-3},
volume = {12},
year = {2019},
}
@article{6840,
abstract = {We discuss thermodynamic properties of harmonically trapped
imperfect quantum gases. The spatial inhomogeneity of these systems imposes
a redefinition of the mean-field interparticle potential energy as compared
to the homogeneous case. In our approach, it takes the form a
2N2 ωd, where
N is the number of particles, ω—the harmonic trap frequency, d—system’s
dimensionality, and a is a parameter characterizing the interparticle interaction.
We provide arguments that this model corresponds to the limiting case of
a long-ranged interparticle potential of vanishingly small amplitude. This
conclusion is drawn from a computation similar to the well-known Kac scaling
procedure, which is presented here in a form adapted to the case of an isotropic
harmonic trap. We show that within the model, the imperfect gas of trapped
repulsive bosons undergoes the Bose–Einstein condensation provided d > 1.
The main result of our analysis is that in d = 1 the gas of attractive imperfect
fermions with a = −aF < 0 is thermodynamically equivalent to the gas of
repulsive bosons with a = aB > 0 provided the parameters aF and aB fulfill
the relation aB + aF = . This result supplements similar recent conclusion
about thermodynamic equivalence of two-dimensional (2D) uniform imperfect
repulsive Bose and attractive Fermi gases.},
author = {Mysliwy, Krzysztof and Napiórkowski, Marek},
issn = {1742-5468},
journal = {Journal of Statistical Mechanics: Theory and Experiment},
number = {6},
publisher = {IOP Publishing},
title = {{Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps}},
doi = {10.1088/1742-5468/ab190d},
volume = {2019},
year = {2019},
}