1,346 research outputs found
The Maximal Denumerant of a Numerical Semigroup
Given a numerical semigroup S = and n in S, we
consider the factorization n = c_0 a_0 + c_1 a_1 + ... + c_t a_t where c_i >=
0. Such a factorization is maximal if c_0 + c_1 + ... + c_t is a maximum over
all such factorizations of n. We provide an algorithm for computing the maximum
number of maximal factorizations possible for an element in S, which is called
the maximal denumerant of S. We also consider various cases that have
connections to the Cohen-Macualay and Gorenstein properties of associated
graded rings for which this algorithm simplifies.Comment: 13 Page
Complete genome sequence of the hippuricase-positive Campylobacter avium Type 5 LMG 24591
cited By 0Campylobacter avium is a thermotolerant Campylobacter species that has been isolated from poultry. C. avium was also the second hippuricase-positive species to be identified within Campylobacter. Here, we present the genome sequence of the C. avium type strain LMG 24591 (= CCUG 56292T), isolated in 2006 from a broiler chicken in Italy. © 2017 Miller et al.Peer reviewe
Modeling the Searching Behavior of Social Monkeys
We discuss various features of the trajectories of spider monkeys looking for
food in a tropical forest, as observed recently in an extensive {\it in situ}
study. Some of the features observed can be interpreted as the result of social
interactions. In addition, a simple model of deterministic walk in a random
environment reproduces the observed angular correlations between successive
steps, and in some cases, the emergence of L\'evy distributions for the length
of the steps.Comment: 7 pages, 3 figure
Structure-function analysis of the curli accessory protein CsgE defines surfaces essential for coordinating amyloid fiber formation
Curli amyloid fibers are produced as part of the extracellular biofilm matrix and are composed primarily of the major structural subunit CsgA. The CsgE chaperone facilitates the secretion of CsgA through CsgG by forming a cap at the base of the nonameric CsgG outer membrane pore. We elucidated a series of finely tuned nonpolar and charge-charge interactions that facilitate the oligomerization of CsgE and its ability to transport unfolded CsgA to CsgG for translocation. CsgE oligomerization in vitro is temperature dependent and is disrupted by mutations in the W48 and F79 residues. Using nuclear magnetic resonance (NMR), we identified two regions of CsgE involved in the CsgE-CsgA interaction: a head comprising a positively charged patch centered around R47 and a stem comprising a negatively charged patch containing E31 and E85. Negatively charged residues in the intrinsically disordered N- and C-terminal “tails” were not implicated in this interaction. Head and stem residues were mutated and interrogated using in vivo measurements of curli production and in vitro amyloid polymerization assays. The R47 head residue of CsgE is required for stabilization of CsgA- and CsgE-mediated curli fiber formation. Mutation of the E31 and E85 stem residues to positively charged side chains decreased CsgE-mediated curli fiber formation but increased CsgE-mediated stabilization of CsgA. No single-amino-acid substitutions in the head, stem, or tail regions affected the ability of CsgE to cap the CsgG pore as determined by a bile salt sensitivity assay. These mechanistic insights into the directed assembly of functional amyloids in extracellular biofilms elucidate possible targets for biofilm-associated bacterial infections.Curli represent a class of functional amyloid fibers produced by Escherichia coli and other Gram-negative bacteria that serve as protein scaffolds in the extracellular biofilm matrix. Despite the lack of sequence conservation among different amyloidogenic proteins, the structural and biophysical properties of functional amyloids such as curli closely resemble those of amyloids associated with several common neurodegenerative diseases. These parallels are underscored by the observation that certain proteins and chemicals can prevent amyloid formation by the major curli subunit CsgA and by alpha-synuclein, the amyloid-forming protein found in Lewy bodies during Parkinson’s disease. CsgA subunits are targeted to the CsgG outer membrane pore by CsgE prior to secretion and assembly into fibers. Here, we use biophysical, biochemical, and genetic approaches to elucidate a mechanistic understanding of CsgE function in curli biogenesis
Stabilization of Hydrodynamic Flows by Small Viscosity Variations
Motivated by the large effect of turbulent drag reduction by minute
concentrations of polymers we study the effects of a weakly space-dependent
viscosity on the stability of hydrodynamic flows. In a recent Letter [Phys.
Rev. Lett. {\bf 87}, 174501, (2001)] we exposed the crucial role played by a
localized region where the energy of fluctuations is produced by interactions
with the mean flow (the "critical layer"). We showed that a layer of weakly
space-dependent viscosity placed near the critical layer can have a very large
stabilizing effect on hydrodynamic fluctuations, retarding significantly the
onset of turbulence. In this paper we extend these observation in two
directions: first we show that the strong stabilization of the primary
instability is also obtained when the viscosity profile is realistic (inferred
from simulations of turbulent flows with a small concentration of polymers).
Second, we analyze the secondary instability (around the time-dependent primary
instability) and find similar strong stabilization. Since the secondary
instability develops around a time-dependent solution and is three-dimensional,
this brings us closer to the turbulent case. We reiterate that the large effect
is {\em not} due to a modified dissipation (as is assumed in some theories of
drag reduction), but due to reduced energy intake from the mean flow to the
fluctuations. We propose that similar physics act in turbulent drag reduction.Comment: 10 pages, 17 figs., REVTeX4, PRE, submitte
Parametric Polyhedra with at least Lattice Points: Their Semigroup Structure and the k-Frobenius Problem
Given an integral matrix , the well-studied affine semigroup
\mbox{ Sg} (A)=\{ b : Ax=b, \ x \in {\mathbb Z}^n, x \geq 0\} can be
stratified by the number of lattice points inside the parametric polyhedra
. Such families of parametric polyhedra appear in
many areas of combinatorics, convex geometry, algebra and number theory. The
key themes of this paper are: (1) A structure theory that characterizes
precisely the subset \mbox{ Sg}_{\geq k}(A) of all vectors b \in \mbox{
Sg}(A) such that has at least solutions. We
demonstrate that this set is finitely generated, it is a union of translated
copies of a semigroup which can be computed explicitly via Hilbert bases
computations. Related results can be derived for those right-hand-side vectors
for which has exactly solutions or fewer
than solutions. (2) A computational complexity theory. We show that, when
, are fixed natural numbers, one can compute in polynomial time an
encoding of \mbox{ Sg}_{\geq k}(A) as a multivariate generating function,
using a short sum of rational functions. As a consequence, one can identify all
right-hand-side vectors of bounded norm that have at least solutions. (3)
Applications and computation for the -Frobenius numbers. Using Generating
functions we prove that for fixed the -Frobenius number can be
computed in polynomial time. This generalizes a well-known result for by
R. Kannan. Using some adaptation of dynamic programming we show some practical
computations of -Frobenius numbers and their relatives
The primary structure of three hemoglobin chains from the indigo snake (Drymarchon corais erebennus, Serpentes): First evidence for αD chains and two β chain types in snakes
The hemoglobin of the indigo snake (Drymarchon corais erebennus, Colubrinae) consists of two components, HbA and HbD, in the ratio of 1:1. They differ in both their alpha and beta chains. The amino acid sequences of both alpha chains (alpha(A) and alpha(D)) and one beta chain (betaI) were determined. The presence of an alpha(D)chain in a snake hemoglobin is described for the first time. A comparison of all snake beta chain sequences revealed the existence of two paralogous beta chain types in snakes as well, which are designated as betaI and betaII type. For the discussion of the physiological properties of Drymarchon hemoglobin, the sequences were compared with those of the human alpha and beta chains and those of the closely related water snake Liophis miliaris where functional data are available. Among the heme contacts, the substitution alpha(D)58(E7)His-->Gln is unusual but most likely without any effect. The residues responsible for the main part of the Bohr effect are the same as in mammalian hemoglobins. In each of the three globin chains only two residues at positions involved in the alpha1/beta2 interface contacts, most important for the stability and the properties of the hemoglobin molecule, are substituted with regard to human hemoglobin. On the contrary, nine, eleven, and six alpha1/beta1 contact residues are replaced in the alpha(A), alpha(D), betaI chains, respectively
The Biology Instrument for the Viking Mars Mission
Two Viking spacecraft have successfully soft landed on the surface of Mars. Each carries, along with other scientific instruments, one biology laboratory with three different experiments designed to search for evidence of living microorganisms in material sampled from the Martian surface. This 15.5-kg biology instrument which occupies a volume of almost 28.3 dm3 is the first to carry out an in situ search for extraterrestrial life on a planet. The three experiments are called the pyrolytic release, labeled release, and gas exchange. The pyrolytic release experiment has the capability to measure the fixation of carbon dioxide or carbon monoxide into organic matter. The labeled release experiment detects metabolic processes by monitoring the production of volatile carbon compounds from a radioactively labeled nutrient mixture. The gas exchange experiment monitors the gas changes in the head space above a soil sample which is either incubated in a humid environment or supplied with a rich organic nutrient solution. Each experiment can analyze a soil sample as it is received from the surface or, as a control, analyze a soil which has been heated to above 160C. Each instrument has the capability to receive four different soils dug from the Martian surface and perform a number of analysis cycles depending on the particular experiment. This paper describes in detail the design and operation of the three experiments and the supporting subsystems
Turbulent diffusion and drift in galactic magnetic fields and the explanation of the knee in the cosmic ray spectrum
We reconsider the scenario in which the knee in the cosmic ray spectrum is
explained as due to a change in the escape mechanism of cosmic rays from the
Galaxy from one dominated by transverse diffusion to one dominated by drifts.
We solve the diffusion equations adopting realistic galactic field models and
using diffusion coefficients appropriate for strong turbulence (with a
Kolmogorov spectrum of fluctuations) and consistent with the assumed magnetic
fields. We show that properly taking into account these effects leads to a
natural explanation of the knee in the spectrum, and a transition towards a
heavier composition above the knee is predicted.Comment: 17 pp., 6 figures; revised version with minor changes. To appear in
JHE
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