211 research outputs found
Theoretical investigation of finite size effects at DNA melting
We investigated how the finiteness of the length of the sequence affects the
phase transition that takes place at DNA melting temperature. For this purpose,
we modified the Transfer Integral method to adapt it to the calculation of both
extensive (partition function, entropy, specific heat, etc) and non-extensive
(order parameter and correlation length) thermodynamic quantities of finite
sequences with open boundary conditions, and applied the modified procedure to
two different dynamical models. We showed that rounding of the transition
clearly takes place when the length of the sequence is decreased. We also
performed a finite-size scaling analysis of the two models and showed that the
singular part of the free energy can indeed be expressed in terms of an
homogeneous function. However, both the correlation length and the average
separation between paired bases diverge at the melting transition, so that it
is no longer clear to which of these two quantities the length of the system
should be compared. Moreover, Josephson's identity is satisfied for none of the
investigated models, so that the derivation of the characteristic exponents
which appear, for example, in the expression of the specific heat, requires
some care
Probabilistic Reconstruction in Compressed Sensing: Algorithms, Phase Diagrams, and Threshold Achieving Matrices
Compressed sensing is a signal processing method that acquires data directly
in a compressed form. This allows one to make less measurements than what was
considered necessary to record a signal, enabling faster or more precise
measurement protocols in a wide range of applications. Using an
interdisciplinary approach, we have recently proposed in [arXiv:1109.4424] a
strategy that allows compressed sensing to be performed at acquisition rates
approaching to the theoretical optimal limits. In this paper, we give a more
thorough presentation of our approach, and introduce many new results. We
present the probabilistic approach to reconstruction and discuss its optimality
and robustness. We detail the derivation of the message passing algorithm for
reconstruction and expectation max- imization learning of signal-model
parameters. We further develop the asymptotic analysis of the corresponding
phase diagrams with and without measurement noise, for different distribution
of signals, and discuss the best possible reconstruction performances
regardless of the algorithm. We also present new efficient seeding matrices,
test them on synthetic data and analyze their performance asymptotically.Comment: 42 pages, 37 figures, 3 appendixe
Hybrid free-surface flows in a two-dimensional channel
Hybrid free-surface flows past disturbances in a two-dimensional channel are identified and studied. The fluid is assumed to be inviscid and incompressible, and the flow to be steady and irrotational. The disturbances consist of a step in the bottom of the channel and a flat object lying on the free-surface (e.g., a sluice gate). A weakly nonlinear one-dimensional analysis is used to classify the possible types of solutions, and nonlinear solutions are obtained numerically by a boundary integral equation method.Benjamin James Binder and Jean-Marc Vanden-Broec
Impact of Single Links in Competitive Percolation -- How complex networks grow under competition
How a complex network is connected crucially impacts its dynamics and
function. Percolation, the transition to extensive connectedness upon gradual
addition of links, was long believed to be continuous but recent numerical
evidence on "explosive percolation" suggests that it might as well be
discontinuous if links compete for addition. Here we analyze the microscopic
mechanisms underlying discontinuous percolation processes and reveal a strong
impact of single link additions. We show that in generic competitive
percolation processes, including those displaying explosive percolation, single
links do not induce a discontinuous gap in the largest cluster size in the
thermodynamic limit. Nevertheless, our results highlight that for large finite
systems single links may still induce observable gaps because gap sizes scale
weakly algebraically with system size. Several essentially macroscopic clusters
coexist immediately before the transition, thus announcing discontinuous
percolation. These results explain how single links may drastically change
macroscopic connectivity in networks where links add competitively.Comment: non-final version, for final see Nature Physics homepag
Tracing Carbon Sources through Aquatic and Terrestrial Food Webs Using Amino Acid Stable Isotope Fingerprinting
Tracing the origin of nutrients is a fundamental goal of food web research but methodological issues associated with current research techniques such as using stable isotope ratios of bulk tissue can lead to confounding results. We investigated whether naturally occurring delta C-13 patterns among amino acids (delta C-13(AA)) could distinguish between multiple aquatic and terrestrial primary production sources. We found that delta C-13(AA) patterns in contrast to bulk delta C-13 values distinguished between carbon derived from algae, seagrass, terrestrial plants, bacteria and fungi. Furthermore, we showed for two aquatic producers that their delta C-13(AA) patterns were largely unaffected by different environmental conditions despite substantial shifts in bulk delta C-13 values. The potential of assessing the major carbon sources at the base of the food web was demonstrated for freshwater, pelagic, and estuarine consumers; consumer delta C-13 patterns of essential amino acids largely matched those of the dominant primary producers in each system. Since amino acids make up about half of organismal carbon, source diagnostic isotope fingerprints can be used as a new complementary approach to overcome some of the limitations of variable source bulk isotope values commonly encountered in estuarine areas and other complex environments with mixed aquatic and terrestrial inputs
Association of candidate pharmacogenetic markers with platinum-induced ototoxicity: PanCareLIFE dataset
Genetic association studies suggest a genetic predisposition for cisplatin-induced ototoxicity. Among other candidate genes, thiopurine methyltransferase (TPMT) is considered a critical gene for susceptibility to cisplatin-induced hearing loss in a pharmacogenetic guideline. The PanCareLIFE cross-sectional cohort study evaluated the genetic associations in a large pan-European population and assessed the diagnostic accuracy of the genetic markers. 1,112 pediatric cancer survivors who had provided biomaterial for genotyping were screened for participation in the pharmacogenetic association study. 900 participants qualified for inclusion. Based on the assessment of original audiograms, patients were assigned to three phenotype categories: no, minor, and clinically relevant hearing loss. Fourteen variants in eleven candidate genes (ABCC3, OTOS, TPMT, SLC22A2, NFE2L2, SLC16A5, LRP2, GSTP1, SOD2, WFS1, and ACYP2) were genotyped. The genotype and phenotype data represent a resource for conducting meta-analyses to derive a more precise pooled estimate of the effects of genes on the risk of hearing loss due to platinum treatment
Association of candidate pharmacogenetic markers with platinum-induced ototoxicity:PanCareLIFE dataset
Genetic association studies suggest a genetic predisposi- tion for cisplatin-induced ototoxicity. Among other candidate genes, thiopurine methyltransferase ( TPMT ) is considered a critical gene for susceptibility to cisplatin-induced hearing loss in a pharmacogenetic guideline. The PanCareLIFE cross- sectional cohort study evaluated the genetic associations in a large pan-European population and assessed the diagnos- tic accuracy of the genetic markers. 1,112 pediatric cancer survivors who had provided biomaterial for genotyping were screened for participation in the pharmacogenetic association study. 900 participants qualified for inclusion. Based on the assessment of original audiograms, patients were assigned to three phenotype categories: no, minor, and clinically relevant hearing loss. Fourteen variants in eleven candidate genes ( ABCC3, OTOS, TPMT, SLC22A2, NFE2L2, SLC16A5, LRP2, GSTP1, SOD2, WFS1, and ACYP2 ) were genotyped. The genotype and phenotype data represent a resource for conducting meta- analyses to derive a more precise pooled estimate of the ef- fects of genes on the risk of hearing loss due to platinum treatment
Fumonisins affect the intestinal microbial homeostasis in broiler chickens, predisposing to necrotic enteritis
Fumonisins (FBs) are mycotoxins produced by Fusarium fungi. This study aimed to investigate the effect of these feed contaminants on the intestinal morphology and microbiota composition, and to evaluate whether FBs predispose broilers to necrotic enteritis. One-day-old broiler chicks were divided into a group fed a control diet, and a group fed a FBs contaminated diet (18.6 mg FB1+ FB2/kg feed). A significant increase in the plasma sphinganine/sphingosine ratio in the FBs-treated group (0.21 +/- 0.016) compared to the control (0.14 +/- 0.014) indicated disturbance of the sphingolipid biosynthesis. Furthermore, villus height and crypt depth of the ileum was significantly reduced by FBs. Denaturing gradient gel electrophoresis showed a shift in the microbiota composition in the ileum in the FBs group compared to the control. A reduced presence of low-GC containing operational taxonomic units in ileal digesta of birds exposed to FBs was demonstrated, and identified as a reduced abundance of Candidatus Savagella and Lactobaccilus spp. Quantification of total Clostridium perfringens in these ileal samples, previous to experimental infection, using cpa gene (alpha toxin) quantification by qPCR showed an increase in C. perfringens in chickens fed a FBs contaminated diet compared to control (7.5 +/- 0.30 versus 6.3 +/- 0.24 log10 copies/g intestinal content). After C. perfringens challenge, a higher percentage of birds developed subclinical necrotic enteritis in the group fed a FBs contaminated diet as compared to the control (44.9 +/- 2.22% versus 29.8 +/- 5.46%)
An attainable global vision for conservation and human well-being
A hopeful vision of the future is a world in which both people and nature thrive, but there is little evidence to support the feasibility of such a vision. We used a global, spatially explicit, systems modeling approach to explore the possibility of meeting the demands of increased populations and economic growth in 2050 while simultaneously advancing multiple conservation goals. Our results demonstrate that if, instead of “business as usual” practices, the world changes how and where food and energy are produced, this could help to meet projected increases in food (54%) and energy (56%) demand while achieving habitat protection (>50% of natural habitat remains unconverted in most biomes globally; 17% area of each ecoregion protected in each country), reducing atmospheric greenhouse-gas emissions consistent with the Paris Climate Agreement (≤1.6°C warming by 2100), ending overfishing, and reducing water stress and particulate air pollution. Achieving this hopeful vision for people and nature is attainable with existing technology and consumption patterns. However, success will require major shifts in production methods and an ability to overcome substantial economic, social, and political challenges
The genomic and transcriptional landscape of primary central nervous system lymphoma
Primary lymphomas of the central nervous system (PCNSL) are mainly diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). Molecular drivers of PCNSL have not been fully elucidated. Here, we profile and compare the whole-genome and transcriptome landscape of 51 CNS lymphomas (CNSL) to 39 follicular lymphoma and 36 DLBCL cases outside the CNS. We find recurrent mutations in JAK-STAT, NFkB, and B-cell receptor signaling pathways, including hallmark mutations in MYD88 L265P (67%) and CD79B (63%), and CDKN2A deletions (83%). PCNSLs exhibit significantly more focal deletions of HLA-D (6p21) locus as a potential mechanism of immune evasion. Mutational signatures correlating with DNA replication and mitosis are significantly enriched in PCNSL. TERT gene expression is significantly higher in PCNSL compared to activated B-cell (ABC)-DLBCL. Transcriptome analysis clearly distinguishes PCNSL and systemic DLBCL into distinct molecular subtypes. Epstein-Barr virus (EBV)+ CNSL cases lack recurrent mutational hotspots apart from IG and HLA-DRB loci. We show that PCNSL can be clearly distinguished from DLBCL, having distinct expression profiles, IG expression and translocation patterns, as well as specific combinations of genetic alterations
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