218 research outputs found
Robust Flows over Time: Models and Complexity Results
We study dynamic network flows with uncertain input data under a robust
optimization perspective. In the dynamic maximum flow problem, the goal is to
maximize the flow reaching the sink within a given time horizon , while flow
requires a certain travel time to traverse an edge.
In our setting, we account for uncertain travel times of flow. We investigate
maximum flows over time under the assumption that at most travel times
may be prolonged simultaneously due to delay. We develop and study a
mathematical model for this problem. As the dynamic robust flow problem
generalizes the static version, it is NP-hard to compute an optimal flow.
However, our dynamic version is considerably more complex than the static
version. We show that it is NP-hard to verify feasibility of a given candidate
solution. Furthermore, we investigate temporally repeated flows and show that
in contrast to the non-robust case (that is, without uncertainties) they no
longer provide optimal solutions for the robust problem, but rather yield a
worst case optimality gap of at least . We finally show that the optimality
gap is at most , where and are newly introduced
instance characteristics and provide a matching lower bound instance with
optimality gap and . The results obtained in
this paper yield a first step towards understanding robust dynamic flow
problems with uncertain travel times
Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion
Type IB DNA topoisomerases cleave and rejoin one strand of the DNA duplex, allowing for the removal of supercoils generated during replication and transcription. In addition, electron microscopy of cellular and viral TopIBāDNA complexes has suggested that the enzyme promotes long-range DNAāDNA crossovers and synapses. Here, we have used the atomic force microscope to visualize and quantify the interaction between vaccinia topoisomerase IB (vTopIB) and DNA. vTopIB was found to form filaments on nicked-circular DNA by intramolecular synapsis of two segments of a single DNA molecule. Measuring the filament length as a function of protein concentration showed that synapsis is a highly cooperative process. At high protein:DNA ratios, synapses between distinct DNA molecules were observed, which led to the formation of large vTopIB-induced DNA clusters. These clusters were observed in the presence of Mg(2+), Ca(2+) or Mn(2+), suggesting that the formation of intermolecular vTopIB-mediated DNA synapsis is favored by screening of the DNA charge
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Fast dynamics of supercoiled DNA revealed by single-molecule experiments.
The dynamics of supercoiled DNA play an important role in various cellular processes such as transcription and replication that involve DNA supercoiling. We present experiments that enhance our understanding of these dynamics by measuring the intrinsic response of single DNA molecules to sudden changes in tension or torsion. The observed dynamics can be accurately described by quasistatic models, independent of the degree of supercoiling initially present in the molecules. In particular, the dynamics are not affected by the continuous removal of the plectonemes. These results set an upper bound on the hydrodynamic drag opposing plectoneme removal, and thus provide a quantitative baseline for the dynamics of bare DNA
Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence
The rate of DNA supercoil removal by human topoisomerase IB (TopIB) is slowed down by the presence of the camptothecin class of antitumor drugs. By preventing religation, these drugs also prolong the lifetime of the covalent TopIBāDNA complex. Here, we use magnetic tweezers to measure the rate of supercoil removal by drug-bound TopIB at a single DNA sequence in real time. This is accomplished by covalently linking camptothecins to a triple helix-forming oligonucleotide that binds at one location on the DNA molecule monitored. Surprisingly, we find that the DNA dynamics with the TopIBādrug interaction restricted to a single DNA sequence are indistinguishable from the dynamics observed when the TopIBādrug interaction takes place at multiple sites. Specifically, the DNA sequence does not affect the instantaneous supercoil removal rate or the degree to which camptothecins increase the lifetime of the covalent complex. Our data suggest that sequence-dependent dynamics need not to be taken into account in efforts to develop novel camptothecins
Small Energy Scale for Mixed-Valent Uranium Materials
We investigate a two-channel Anderson impurity model with a magnetic
and a quadrupolar ground doublet, and a excited triplet. Using
the numerical renormalization group method, we find a crossover to a non-Fermi
liquid state below a temperature varying as the triplet-doublet
splitting to the 7/2 power. To within numerical accuracy, the non-linear
magnetic susceptibility and the contribution to the linear
susceptibility are given by universal one-parameter scaling functions. These
results may explain UBe as mixed valent with a small crossover scale
.Comment: 4 pages, 3 figures, REVTeX, to appear in Phys. Rev. Let
Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide SNP data
The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have
been kept geographically and genetically distinct. Due to country-specific selection and
breeding strategies, there is a need to characterize the populations on a genetic level. In
this study we analysed genetic variability of Angora goats from three distinct geographical
regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26;
SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all
autosomes per population were calculated. Diversity, as measured by expected heterozygosity
(HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA
goats were the only population with a positive average inbreeding coefficient value of 0.009.
After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for
further analyses. Principal component and clustering analyses were used to visualize individual
relationships within and between populations. All SA Angora goats were separated
from the others and formed a well-defined, unique cluster, while outliers were identified in
the FR and AR breeds. Apparent admixture between the AR and FR populations was
observed, while both these populations showed signs of having some common ancestry
with the SA goats. LD averaged over adjacent loci within the three populations per chromosome
were calculated. The highest LD values estimated across populations were observed
in the shorter intervals across populations. The Ne for the Angora breed was estimated to
be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness
between the populations.S1 Fig. Admixture plots for K = 2ā4 showing population structure of different Angora subpopulations.The authors thank Margarita Cano (supplying Argentinean Angora DNA samples), Hector
Taddeo (for historical information on the Argentinian Angora breed) and Capgenes (supplying
French Angora DNA samples and historical information on the French Angora breed).The Argentinian part (MP) of the project
was financially supported by Instituto Nacional de
Tecnologia Agropecuaria PNBIO1131033 project.
The South African researchers acknowledge the
National Research Foundation (grants
KIC14011761093 (CV) and TP13073024535
(EVMK)) and the University of Pretoria Genomics
Research Institute (CV) for financial support.http://www.plosone.orgam2016Animal and Wildlife Science
Size, growth and mortality of riverine golden perch (Macquaria ambigua) across a latitudinal gradient
Effective fisheries management requires fish size, growth and mortality information representative of the population and location of interest. Golden perch Macquaria ambigua is long lived, potamodromous and widespread in the MurrayāDarling Basin (MDB), Australia. Using a sample spanning 13 river systems and 10Ā° of latitude, we examined whether the maximum size of golden perch differed by latitude and whether growth and mortality varied between northern and southern MDB regions. The length, weight and age ranges of golden perch sampled (nĀ =Ā 873) were 52ā559Ā mm, 2ā3201Ā g and 0+ to 26+ years respectively, and maximum length and weight were unaffected by latitude. Length and ageālength distributions represented by ageālength keys varied by region, with greater variability in age-at-length and a larger proportion of smaller individuals in northern MDB rivers, which generally exhibit greater variability in discharge. Growth and mortality rates were similar between regions, and an MDB-wide von Bertalanffy growth model (LāĀ =Ā 447, kĀ =Ā 0.32 and t0Ā =Ā ā0.51) and instantaneous mortality rate (ZĀ =Ā 0.20) best described the data. An MDB-wide lengthāweight equation also provided the best fit (WĀ =Ā 6.76Ā ĆĀ 10ā6 L3.12). Our data suggest that the MDB can be treated as one management unit in terms of golden perch maximum size, growth and mortality parameters
2017 EACTS/EACTA Guidelines on patient blood management for adult cardiac surgery
Authors/Task Force Members: Christa Boer (EACTA Chairperson)(Netherlands), Michael I. Meesters (Netherlands), Milan Milojevic (Netherlands), Umberto Benedetto (UK), Daniel Bolliger (Switzerland), Christian von Heymann (Germany), Anders Jeppsson (Sweden), Andreas Koster (Germany), Ruben L. Osnabrugge (Netherlands), Marco Ranucci (Italy), Hanne Berg Ravn (Denmark), Alexander B.A. Vonk (Netherlands), Alexander Wahba (Norway), Domenico Pagano (EACTS Chairperson)(UK),. Document Reviewers: Moritz W.V. Wyler von Ballmoos (USA), Mate Petricevic (Croatia), Arie Pieter Kappetein (Netherlands), Miguel Sousa-Uva (Portugal), Georg Trummer (Germany), Peter M. Rosseel (Netherlands), Michael Sander (Germany), Pascal Colson (France), Adrian Bauer (Germany)
Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
To support efforts to develop a āsynthetic biologyā based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1ā²-Ī²-D-2ā²-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its WatsonāCrick complement, the purine analog 2-amino-8-(1ā²-Ī²-D-2ā²-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where āpyā indicates a pyrimidine analog and āpuā indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA
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