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The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus.
Filamentous fungi, such as Neurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling of N. crassa on 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors in N. crassa and characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level
Associahedra via spines
An associahedron is a polytope whose vertices correspond to triangulations of
a convex polygon and whose edges correspond to flips between them. Using
labeled polygons, C. Hohlweg and C. Lange constructed various realizations of
the associahedron with relevant properties related to the symmetric group and
the classical permutahedron. We introduce the spine of a triangulation as its
dual tree together with a labeling and an orientation. This notion extends the
classical understanding of the associahedron via binary trees, introduces a new
perspective on C. Hohlweg and C. Lange's construction closer to J.-L. Loday's
original approach, and sheds light upon the combinatorial and geometric
properties of the resulting realizations of the associahedron. It also leads to
noteworthy proofs which shorten and simplify previous approaches.Comment: 27 pages, 11 figures. Version 5: minor correction
Literature-based discovery of diabetes- and ROS-related targets
Abstract Background Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the genes associated with ROS. Methods We present ROS- and diabetes-related targets (genes/proteins) collected from the biomedical literature through a text mining technology. A web-based literature mining tool, SciMiner, was applied to 1,154 biomedical papers indexed with diabetes and ROS by PubMed to identify relevant targets. Over-represented targets in the ROS-diabetes literature were obtained through comparisons against randomly selected literature. The expression levels of nine genes, selected from the top ranked ROS-diabetes set, were measured in the dorsal root ganglia (DRG) of diabetic and non-diabetic DBA/2J mice in order to evaluate the biological relevance of literature-derived targets in the pathogenesis of diabetic neuropathy. Results SciMiner identified 1,026 ROS- and diabetes-related targets from the 1,154 biomedical papers (http://jdrf.neurology.med.umich.edu/ROSDiabetes/). Fifty-three targets were significantly over-represented in the ROS-diabetes literature compared to randomly selected literature. These over-represented targets included well-known members of the oxidative stress response including catalase, the NADPH oxidase family, and the superoxide dismutase family of proteins. Eight of the nine selected genes exhibited significant differential expression between diabetic and non-diabetic mice. For six genes, the direction of expression change in diabetes paralleled enhanced oxidative stress in the DRG. Conclusions Literature mining compiled ROS-diabetes related targets from the biomedical literature and led us to evaluate the biological relevance of selected targets in the pathogenesis of diabetic neuropathy.http://deepblue.lib.umich.edu/bitstream/2027.42/78315/1/1755-8794-3-49.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/2/1755-8794-3-49-S7.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/3/1755-8794-3-49-S10.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/4/1755-8794-3-49-S8.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/5/1755-8794-3-49-S3.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/6/1755-8794-3-49-S1.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/7/1755-8794-3-49-S4.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/8/1755-8794-3-49-S2.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/9/1755-8794-3-49-S12.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/10/1755-8794-3-49-S11.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/11/1755-8794-3-49-S9.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/12/1755-8794-3-49-S5.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/13/1755-8794-3-49-S6.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/14/1755-8794-3-49.pdfPeer Reviewe
Asymptotic models for the generation of internal waves by a moving ship, and the dead-water phenomenon
This paper deals with the dead-water phenomenon, which occurs when a ship
sails in a stratified fluid, and experiences an important drag due to waves
below the surface. More generally, we study the generation of internal waves by
a disturbance moving at constant speed on top of two layers of fluids of
different densities. Starting from the full Euler equations, we present several
nonlinear asymptotic models, in the long wave regime. These models are
rigorously justified by consistency or convergence results. A careful
theoretical and numerical analysis is then provided, in order to predict the
behavior of the flow and in which situations the dead-water effect appears.Comment: To appear in Nonlinearit
Finite Temperature Perturbation Theory for a Spatially Inhomogeneous Bose-condensed Gas
We develop a finite temperature perturbation theory (beyond the mean field)
for a Bose-condensed gas and calculate temperature-dependent damping rates and
energy shifts for Bogolyubov excitations of any energy. The theory is
generalized for the case of excitations in a spatially inhomogeneous (trapped)
Bose-condensed gas, where we emphasize the principal importance of
inhomogeneouty of the condensate density profile and develop the method of
calculating the self-energy functions. The use of the theory is demonstrated by
calculating the damping rates and energy shifts of low-energy quasiclassical
excitations, i.e. the quasiclassical excitations with energies much smaller
than the mean field interaction between particles. In this case the boundary
region of the condensate plays a crucial role, and the result for the damping
rates and energy shifts is completely different from that in spatially
homogeneous gases. We also analyze the frequency shifts and damping of sound
waves in cylindrical Bose condensates and discuss the role of damping in the
recent MIT experiment on the sound propagation.Comment: 16 pages, 3 figures, Revtex, uses epsfi
Multi-triangulations as complexes of star polygons
Maximal -crossing-free graphs on a planar point set in convex
position, that is, -triangulations, have received attention in recent
literature, with motivation coming from several interpretations of them.
We introduce a new way of looking at -triangulations, namely as complexes
of star polygons. With this tool we give new, direct, proofs of the fundamental
properties of -triangulations, as well as some new results. This
interpretation also opens-up new avenues of research, that we briefly explore
in the last section.Comment: 40 pages, 24 figures; added references, update Section
Identifying barriers to patient acceptance of active surveillance: content analysis of online patient communications.
OBJECTIVES: Qualitative research aimed at identifying patient acceptance of active surveillance (AS) has been identified as a public health research priority. The primary objective of this study was to determine if analysis of a large-sample of anonymous internet conversations (ICs) could be utilized to identify unmet public needs regarding AS.
METHODS: English-language ICs regarding prostate cancer (PC) treatment with AS from 2002-12 were identified using a novel internet search methodology. Web spiders were developed to mine, aggregate, and analyze content from the world-wide-web for ICs centered on AS. Collection of ICs was not restricted to any specific geographic region of origin. NLP was used to evaluate content and perform a sentiment analysis. Conversations were scored as positive, negative, or neutral. A sentiment index (SI) was subsequently calculated according to the following formula to compare temporal trends in public sentiment towards AS: [(# Positive IC/#Total IC)-(#Negative IC/#Total IC) x 100].
RESULTS: A total of 464 ICs were identified. Sentiment increased from -13 to +2 over the study period. The increase sentiment has been driven by increased patient emphasis on quality-of-life factors and endorsement of AS by national medical organizations. Unmet needs identified in these ICs include: a gap between quantitative data regarding long-term outcomes with AS vs. conventional treatments, desire for treatment information from an unbiased specialist, and absence of public role models managed with AS.
CONCLUSIONS: This study demonstrates the potential utility of online patient communications to provide insight into patient preferences and decision-making. Based on our findings, we recommend that multidisciplinary clinics consider including an unbiased specialist to present treatment options and that future decision tools for AS include quantitative data regarding outcomes after AS
Vortex dynamics for two-dimensional XY models
Two-dimensional XY models with resistively shunted junction (RSJ) dynamics
and time dependent Ginzburg-Landau (TDGL) dynamics are simulated and it is
verified that the vortex response is well described by the Minnhagen
phenomenology for both types of dynamics. Evidence is presented supporting that
the dynamical critical exponent in the low-temperature phase is given by
the scaling prediction (expressed in terms of the Coulomb gas temperature
and the vortex renormalization given by the dielectric constant
) both for RSJ and TDGL
and that the nonlinear IV exponent a is given by a=z+1 in the low-temperature
phase. The results are discussed and compared with the results of other recent
papers and the importance of the boundary conditions is emphasized.Comment: 21 pages including 15 figures, final versio
Role of heavy-meson exchange in pion production near threshold
Recent calculations of -wave pion production have severely underestimated
the accurately known \ total cross section near
threshold. In these calculations, only the single-nucleon axial-charge operator
is considered. We have calculated, in addition to the one-body term, the
two-body contributions to this reaction that arise from the exchange of mesons.
We find that the inclusion of the scalar -meson exchange current (and
lesser contributions from other mesons) increases the cross section by about a
factor of five, and leads to excellent agreement with the data. The results are
neither very sensitive to changes in the distorting potential that generates
the wave function, nor to different choices for the meson-nucleon form
factors. We argue that \ data provide direct
experimental evidence for meson-exchange contributions to the axial current.Comment: 28 Pages, IU-NTC #93-0
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