530 research outputs found

### ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures

ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. These proteins are of interest to a wide range of biologists due to their diverse applications in medicine, neuroscience, pharmacology, drug discovery and agriculture. ArachnoServer currently manages 1078 protein sequences, 759 nucleic acid sequences and 56 protein structures. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface. The following significant improvements have been implemented in version 2.0: (i) the average and monoisotopic molecular masses of both the reduced and oxidized form of each mature toxin are provided; (ii) the advanced search feature now enables searches on the basis of toxin mass, external database accession numbers and publication date in ArachnoServer; (iii) toxins can now be browsed on the basis of their phyletic specificity; (iv) rapid BLAST searches based on the mature toxin sequence can be performed directly from the toxin card; (v) private silos can be requested from research groups engaged in venoms-based research, enabling them to easily manage and securely store data during the process of toxin discovery; and (vi) a detailed user manual is now available

### Resolution of the paradox of the diamagnetic effect on the Kibble Coil

Employing very simple electro-mechanical principles known from classical physics, the Kibble balance establishes a very precise and absolute link between quantum electrical standards and macroscopic mass or force measurements. The success of the Kibble balance, in both determining fundamental constants (h, NA, e) and realizing a quasi-quantum mass in the 2019 newly revised International System of Units, relies on the perfection of Maxwell’s equations and the symmetry they describe between Lorentz’s force and Faraday’s induction, a principle and a symmetry stunningly demonstrated in the weighing and velocity modes of Kibble balances to within 1×10−8, with nothing but imperfect wires and magnets. However, recent advances in the understanding of the current effect in Kibble balances reveal a troubling paradox. A diamagnetic effect, a force that does not cancel between mass-on and mass-off measurement, is challenging balance maker’s assumptions of symmetry at levels that are almost two orders of magnitude larger than the reported uncertainties. The diamagnetic effect, if it exists, shows up in weighing mode without a readily apparent reciprocal effect in the velocity mode, begging questions about systematic errors at the very foundation of the new measurement system. The hypothetical force is caused by the coil current changing the magnetic field, producing an unaccounted force that is systematically modulated with the weighing current. Here we show that this diamagnetic force exists, but the additional force does not change the equivalence between weighing and velocity measurements. We reveal the unexpected way that symmetry is preserved and show that for typical materials and geometries the total relative effect on the measurement is ≈1×10−9

### On a Camassa-Holm type equation with two dependent variables

We consider a generalization of the Camassa Holm (CH) equation with two
dependent variables, called CH2, introduced by Liu and Zhang. We briefly
provide an alternative derivation of it based on the theory of Hamiltonian
structures on (the dual of) a Lie Algebra. The Lie Algebra here involved is the
same algebra underlying the NLS hierarchy. We study the structural properties
of the CH2 hierarchy within the bihamiltonian theory of integrable PDEs, and
provide its Lax representation. Then we explicitly discuss how to construct
classes of solutions, both of peakon and of algebro-geometrical type. We
finally sketch the construction of a class of singular solutions, defined by
setting to zero one of the two dependent variables.Comment: 22 pages, 2 figures. A few typos correcte

### Symbolic Software for the Painleve Test of Nonlinear Ordinary and Partial Differential Equations

The automation of the traditional Painleve test in Mathematica is discussed.
The package PainleveTest.m allows for the testing of polynomial systems of
ordinary and partial differential equations which may be parameterized by
arbitrary functions (or constants). Except where limited by memory, there is no
restriction on the number of independent or dependent variables. The package is
quite robust in determining all the possible dominant behaviors of the Laurent
series solutions of the differential equation. The omission of valid dominant
behaviors is a common problem in many implementations of the Painleve test, and
these omissions often lead to erroneous results. Finally, our package is
compared with the other available implementations of the Painleve test.Comment: Published in the Journal of Nonlinear Mathematical Physics
(http://www.sm.luth.se/math/JNMP/), vol. 13(1), pp. 90-110 (Feb. 2006). The
software can be downloaded at either http://www.douglasbaldwin.com or
http://www.mines.edu/fs_home/wherema

### Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins efforts to improve early detection and treatment outcomes. While large EAC exome sequencing efforts to date have found recurrent loss-offunction mutations, oncogenic driving events have been underrepresented. Here we use a combination of whole-genome sequencing (WGS) and single-nucleotide polymorphism-array profiling to show that genomic catastrophes are frequent in EAC, with almost a third (32%, n¼40/123) undergoing chromothriptic events. WGS of 22 EAC cases show that catastrophes may lead to oncogene amplification through chromothripsis-derived double-minute chromosome formation (MYC and MDM2) or breakage-fusion-bridge (KRAS, MDM2 and RFC3). Telomere shortening is more prominent in EACs bearing localized complex rearrangements. Mutational signature analysis also confirms that extreme genomic instability in EAC can be driven by somatic BRCA2 mutations. These findings suggest that genomic catastrophes have a significant role in the malignant transformation of EAC

### ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures

ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. These proteins are of interest to a wide range of biologists due to their diverse applications in medicine, neuroscience, pharmacology, drug discovery and agriculture. ArachnoServer currently manages 1078 protein sequences, 759 nucleic acid sequences and 56 protein structures. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface. The following significant improvements have been implemented in version 2.0: (i) the average and monoisotopic molecular masses of both the reduced and oxidized form of each mature toxin are provided; (ii) the advanced search feature now enables searches on the basis of toxin mass, external database accession numbers and publication date in ArachnoServer; (iii) toxins can now be browsed on the basis of their phyletic specificity; (iv) rapid BLAST searches based on the mature toxin sequence can be performed directly from the toxin card; (v) private silos can be requested from research groups engaged in venoms-based research, enabling them to easily manage and securely store data during the process of toxin discovery; and (vi) a detailed user manual is now available

### Renormalization group approach to multiscale modelling in materials science

Dendritic growth, and the formation of material microstructure in general,
necessarily involves a wide range of length scales from the atomic up to sample
dimensions. The phase field approach of Langer, enhanced by optimal asymptotic
methods and adaptive mesh refinement, copes with this range of scales, and
provides an effective way to move phase boundaries. However, it fails to
preserve memory of the underlying crystallographic anisotropy, and thus is
ill-suited for problems involving defects or elasticity. The phase field
crystal (PFC) equation-- a conserving analogue of the Hohenberg-Swift equation
--is a phase field equation with periodic solutions that represent the atomic
density. It can natively model elasticity, the formation of solid phases, and
accurately reproduces the nonequilibrium dynamics of phase transitions in real
materials. However, the PFC models matter at the atomic scale, rendering it
unsuitable for coping with the range of length scales in problems of serious
interest. Here, we show that a computationally-efficient multiscale approach to
the PFC can be developed systematically by using the renormalization group or
equivalent techniques to derive appropriate coarse-grained coupled phase and
amplitude equations, which are suitable for solution by adaptive mesh
refinement algorithms

### On the (Non)-Integrability of KdV Hierarchy with Self-consistent Sources

Non-holonomic deformations of integrable equations of the KdV hierarchy are
studied by using the expansions over the so-called "squared solutions" (squared
eigenfunctions). Such deformations are equivalent to perturbed models with
external (self-consistent) sources. In this regard, the KdV6 equation is viewed
as a special perturbation of KdV equation. Applying expansions over the
symplectic basis of squared eigenfunctions, the integrability properties of the
KdV hierarchy with generic self-consistent sources are analyzed. This allows
one to formulate a set of conditions on the perturbation terms that preserve
the integrability. The perturbation corrections to the scattering data and to
the corresponding action-angle variables are studied. The analysis shows that
although many nontrivial solutions of KdV equations with generic
self-consistent sources can be obtained by the Inverse Scattering Transform
(IST), there are solutions that, in principle, can not be obtained via IST.
Examples are considered showing the complete integrability of KdV6 with
perturbations that preserve the eigenvalues time-independent. In another type
of examples the soliton solutions of the perturbed equations are presented
where the perturbed eigenvalue depends explicitly on time. Such equations,
however in general, are not completely integrable.Comment: 16 pages, no figures, LaTe

### Radiative Decays of the Upsilon(1S) to a Pair of Charged Hadrons

Using data obtained with the CLEO~III detector, running at the Cornell
Electron Storage Ring (CESR), we report on a new study of exclusive radiative
Upsilon(1S) decays into the final states gamma pi^+ pi^-, gamma K^+ K^-, and
gamma p pbar.. We present branching ratio measurements for the decay modes
Upsilon(1S) to gamma f_2(1270), Upsilon(1S) to gamma f_2'(1525), and
Upsilon(1S) to gamma K^+K^-; helicity production ratios for f_2(1270) and
f_2'(1525); upper limits for the decay Upsilon(1S) to gamma f_J(2200), with
f_J(2220) to pi^+ pi^-, K^+ K^-, p pbar; and an upper limit for the decay
Upsilon(1S) to gamma X(1860), with X(1860) to gamma p pbar.Comment: 17 pages postscript,also available through
http://www.lns.cornell.edu/public/CLNS/2005/, Submitted to PR

### The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens

Background
Campylobacters are an unwelcome member of the poultry gut microbiota in terms of food safety. The objective of this study was to compare the microbiota, inflammatory responses, and zootechnical parameters of broiler chickens not exposed to Campylobacter jejuni with those exposed either early at 6 days old or at the age commercial broiler chicken flocks are frequently observed to become colonized at 20 days old.
Results
Birds infected with Campylobacter at 20 days became cecal colonized within 2 days of exposure, whereas birds infected at 6 days of age did not show complete colonization of the sample cohort until 9 days post-infection. All birds sampled thereafter were colonized until the end of the study at 35 days (mean 6.1 log10 CFU per g of cecal contents). The cecal microbiota of birds infected with Campylobacter were significantly different to age-matched non-infected controls at 2 days post-infection but generally the composition of the cecal microbiota were more affected by bird age as the time post infection increased. The effects of Campylobacter colonization on the cecal microbiota were associated with reductions in the relative abundance of OTUs within the taxonomic family Lactobacillaceae and the Clostridium cluster XIVa. Specific members of the Lachnospiraceae and Ruminococcaceae families exhibit transient shifts in microbial community populations dependent upon the age at which the birds become colonized by C. jejuni. Analysis of ileal and cecal chemokine/cytokine gene expression revealed increases in IL-6, IL-17A and Il-17F consistent with a Th17 response but the persistence of the response was dependent on the stage/time of C. jejuni colonization that coincide with significant reductions in the abundance of Clostridium cluster XIVa.
Conclusions
This study combines microbiome data, cytokine/chemokine gene expression with intestinal villus and crypt measurements to compare chickens colonized early or late in the rearing cycle to provide insights into the process and outcomes of Campylobacter colonization. Early colonization results in a transient growth rate reduction and pro-inflammatory response but persistent modification of the cecal microbiota. Late colonization produces pro-inflammatory responses with changes in the cecal microbiota that will endure in market ready chickens

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