On the Average Genus of a Graph

Not all rational numbers are possibilities for the average genus of an individual graph. The smallest such numbers are determined, and varied examples are constructed to demonstrate that a single value of average genus can be shared by arbitrarily many different graphs. It is proved that the number one is a limit point of the set of possible values for average genus and that the complete graph K4 is the only 3-connected graph whose average genus is less than one. Several problems for future study are suggested

Immunohistochemical Distribution of PlexinA4 in the Adult Rat Central Nervous System

PlexinA4 is the latest member to be identified of the PlexinA subfamily, critical transducers of class 3 semaphorin signaling as co-receptors to neuropilins 1 and 2. Despite functional information regarding the role of PlexinA4 in development and guidance of specific neuronal pathways, little is known about its distribution in the adult central nervous system (CNS). Here we report an in depth immunohistochemical analysis of PlexinA4 expression in the adult rat CNS. PlexinA4 staining was present in neurons and fibers throughout the brain and spinal cord, including neocortex, hippocampus, lateral hypothalamus, red nucleus, facial nucleus, and the mesencephalic trigeminal nucleus. PlexinA4 antibodies labeled fibers in the lateral septum, nucleus accumbens, several thalamic nuclei, substantia nigra pars reticulata, zona incerta, pontine reticular region, as well as in several cranial nerve nuclei. This constitutes the first detailed description of the topographic distribution of PlexinA4 in the adult CNS and will set the basis for future studies on the functional implications of PlexinA4 in adult brain physiology

Violation of the `Zero-Force Theorem' in the time-dependent Krieger-Li-Iafrate approximation

We demonstrate that the time-dependent Krieger-Li-Iafrate approximation in combination with the exchange-only functional violates the `Zero-Force Theorem'. By analyzing the time-dependent dipole moment of Na5 and Na9+, we furthermore show that this can lead to an unphysical self-excitation of the system depending on the system properties and the excitation strength. Analytical aspects, especially the connection between the `Zero-Force Theorem' and the `Generalized-Translation Invariance' of the potential, are discussed.Comment: 5 pages, 4 figure

Effects of CarbonDioxide on Rainbow Trout Larvae: Application for Invasive Fish Eradication

Currently, efforts are underway to eradicate invasive fish species that threaten the ecological integrity of aquatic ecosystems. Several studies have examined the effects of anesthetizing fish for easier handling, surgical procedures, tagging and management. Carbon Dioxide (CO2) is an approved and efficient anesthetic for adult fish in medicine and aquaculture and is favorable due to lack of residues, zero withdrawal period and does not need to be registered as its classification is generally regarded as safe (GRAS). Carbon dioxide has also shown to have lethal effects on other life history stages of fish. In this study, various early life stages of Rainbow trout (Oncorhynchus mykiss) larvae were exposed to CO2 in the form of dry ice pellets to determine the critical period of sensitivity for mortality in a model salmonid species. Studies were conducted in aluminum tanks (n = 3 tanks per treatment, with three chambers in each tank with 40 larvae per chamber) with 68 liters of filtered creek water (dissolved CO2 = 4 mg/l, dissolved O2 = 8.125 mg/l, pH = 7.78, temperature = 12.9°C, conductivity = -55 mV, Total alkalinity as CaCO3 = 160 mg/l). Larvae exposed at post hatch day 10 had increased susceptibility to CO2, when compared with earlier embryonic stages. The results of the experiment indicate that early rainbow trout life history stages are susceptible to CO2 but only at late embryonic stages and may have implications for systematically eradicating invasive salmonids

The Effects of Ultraviolet Light on Rainbow Trout Embryos

There currently exists a need to develop new approaches to control aquatic invasive and nuisance species. The effects of light radiation such as ultra-violet wavelengths of light have shown negative effects, such as increased embryo mortality in early embryonic salmonid larvae. This study explores the use of light radiation for eradication of invasive fish. Experiments were conducted to evaluate dose and critical period of sensitivity for mortality of rainbow trout (Oncorhynchus mykiss) embryos after exposure to visual and ultra-violet light radiation. Endpoints recorded include exposure intensity, effective distance from source, duration of exposure, malformations and mortality. Introduced light may be an effective and feasible eradication technique of early life history stages of fish and invertebrate invasive species in situ, as light can be implemented and removed with minimal environmental impact

SCOPE: a web server for practical de novo motif discovery

SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a set of gene names or FASTA sequences and a choice of species. The most significant motifs found by SCOPE are displayed graphically on the main results page with a table containing summary statistics for each motif. Detailed motif information, including the sequence logo, PWM, consensus sequence and specific matching sites can be viewed through a single click on a motif. SCOPE's efficient, parameter-free search strategy has enabled the development of a web server that is readily accessible to the practising biologist while providing results that compare favorably with those of other motif finders. The SCOPE web server is at <http://genie.dartmouth.edu/scope>

A Rigorous Derivation of the Gross-Pitaevskii Energy Functional for a Two-Dimensional Bose Gas

We consider the ground state properties of an inhomogeneous two-dimensional Bose gas with a repulsive, short range pair interaction and an external confining potential. In the limit when the particle number $N$ is large but $\bar\rho a^2$ is small, where $\bar\rho$ is the average particle density and $a$ the scattering length, the ground state energy and density are rigorously shown to be given to leading order by a Gross-Pitaevskii (GP) energy functional with a coupling constant $g\sim 1/|\ln(\bar\rho a^2)|$. In contrast to the 3D case the coupling constant depends on $N$ through the mean density. The GP energy per particle depends only on $Ng$. In 2D this parameter is typically so large that the gradient term in the GP energy functional is negligible and the simpler description by a Thomas-Fermi type functional is adequate.Comment: 14 pages, no figures, latex 2e. References, some clarifications and an appendix added. To appear in Commun. Math. Phy

Native Electrospray and Electron-Capture Dissociation in FTICR Mass Spectrometry Provide Top-Down Sequencing of a Protein Component in an Intact Protein Assembly

The intact yeast alcohol dehydrogenase (ADH) tetramer of 147 kDa was introduced into a FTICR mass spectrometer by native electrospray. Electron capture dissociation of the entire 23+ to 27+ charge state distribution produced the expected charge-reduced ions and, more unexpectedly, 39 c-type peptide fragments that identified N-terminus acetylation and the first 55 amino acids. The results are in accord with the crystal structure of yeast ADH, which shows that the C-terminus is buried at the assembly interface, whereas the N-terminus is exposed, allowing ECD to occur. This remarkable observation shows promise that a top-down approach for intact protein assemblies will be effective for characterizing their components, inferring their interfaces, and obtaining both proteomics and structural biology information in one experiment