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