On the Mechanism of Townsend Avalanche for Negative Molecular Ions

Time projection chambers drifting negative ions (NITPC) instead of electrons have several advantages. A NITPC can operate at very high reduced drift fields without diffusion runaway, and the readout digitization sampling rate requirement is considerably relaxed due to the low drift speed of negative ions. The initiation of Townsend avalanches to allow gas gain in these devices has not been understood until now. It is shown here that the avalanche in low pressure CS$_2$ vapor is most likely initiated by collisional detachment of the electron from the negative molecular ion. In mixtures of Nitromethane vapor with CO$_2$ the mechanism appears to be more complex

Deductive Pluralism

This paper proposes an approach to the philosophy of mathematics, deductive pluralism, that is designed to satisfy the criteria of inclusiveness of and consistency with mathematical practice. Deductive pluralism views mathematical statements as assertions that a result follows from logical and mathematical foundations and that there are a variety of incompatible foundations such as standard foundations, constructive foundations, or univalent foundations. The advantages of this philosophy include the elimination of ontological problems, epistemological clarity, and objectivity. Possible objections and relations with some other philosophies of mathematics are also considered

A benign, low Z electron capture agent for negative ion TPCs

We have identified nitromethane (CH$_3$NO$_2$) as an effective electron capture agent for negative ion TPCs (NITPCs). We present drift velocity and longitudinal diffusion measurements for negative ion gas mixtures using nitromethane as the capture agent. Not only is nitromethane substantially more benign than the only other identified capture agent, CS$_2$, but its low atomic number will enable the use of the NITPC as a photoelectric X{}-ray polarimeter in the 1{}-10 keV band

Deductive Pluralism

This paper proposes an approach to the philosophy of mathematics, deductive pluralism, that satisfies the criterion of inclusiveness of mathematical practice. The basic argument is as follows: there are existing varieties of mathematics with incompatible foundations; given these varieties, a philosophy of mathematics should be inclusive; the criterion of inclusiveness and the fact of incompatible varieties implies a pluralistic philosophy; this in turn requires a deductivist approach within each variety; thus deductive pluralism. The advantages of deductive pluralism include the elimination of ontological problems, epistemological clarity, and objectivity

Panel: Grant Writing

Grant writing has become a major component of many academicians’ careers. As funding for projects becomes scarce at colleges and universities, external grants provide an excellent opportunity to fund small to large research studies that have an impact across a variety of fields and contexts. This panel will explore the process of grant writing, including locating, planning, writing, reviewing, and managing grants. The panelists provide a wide variety of grant writing experience. In particular the panel will cover topics include locating, planning, writing, reviewing, and managing a grant. Each panelist will highlight the following when discussing each topic: What are possible approaches when targeting a particular agency? How to match your research to fit with a request for proposal? How to avoid key pitfalls when pursuing external funding

PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations

Derivation of biological meaning from large sets of proteins or genes is a frequent task in genomic and proteomic studies. Such sets often arise from experimental methods including large-scale gene expression experiments and mass spectrometry (MS) proteomics. Large sets of genes or proteins are also the outcome of computational methods such as BLAST search and homology-based classifications. We have developed the PANDORA web server, which functions as a platform for the advanced biological analysis of sets of genes, proteins, or proteolytic peptides. First, the input set is mapped to a set of corresponding proteins. Then, an analysis of the protein set produces a graph-based hierarchy which highlights intrinsic relations amongst biological subsets, in light of their different annotations from multiple annotation resources. PANDORA integrates a large collection of annotation sources (GO, UniProt Keywords, InterPro, Enzyme, SCOP, CATH, Gene-3D, NCBI taxonomy and more) that comprise ∼200 000 different annotation terms associated with ∼3.2 million sequences from UniProtKB. Statistical enrichment based on a binomial approximation of the hypergeometric distribution and corrected for multiple hypothesis tests is calculated using several background sets, including major gene-expression DNA-chip platforms. Users can also visualize either standard or user-defined binary and quantitative properties alongside the proteins. PANDORA 4.2 is available at http://www.pandora.cs.huji.ac.il

Effects of Ignoring Survey Design Information for Data Reuse

Data are currently being used, and reused, in ecological research at an unprecedented rate. To ensure appropriate reuse however, we need to ask the question: "Are aggregated databases currently providing the right information to enable effective and unbiased reuse?" We investigate this question, with a focus on designs that purposefully favor the selection of sampling locations (upweighting the probability of selection of some locations). These designs are common and examples are those designs that have uneven inclusion probabilities or are stratified. We perform a simulation experiment by creating data sets with progressively more uneven inclusion probabilities and examine the resulting estimates of the average number of individuals per unit area (density). The effect of ignoring the survey design can be profound, with biases of up to 250% in density estimates when naive analytical methods are used. This density estimation bias is not reduced by adding more data. Fortunately, the estimation bias can be mitigated by using an appropriate estimator or an appropriate model that incorporates the design information. These are only available however, when essential information about the survey design is available: the sample location selection process (e.g., inclusion probabilities), and/or covariates used in their specification. The results suggest that such information must be stored and served with the data to support meaningful inference and data reuse.Peer reviewe

Association of Juvenile Salmon and Estuarine Fish with Intertidal Seagrass and Oyster Aquaculture Habitats in a Northeast Pacific Estuary

Structured estuarine habitats, such as salt marshes, seagrass beds, and oyster reefs, are recognized as critical nurseries for juvenile fish and crustaceans. Estuarine habitat usage by fish, including juvenile Pacific salmon Oncorhynchus spp., was characterized by sampling with a modified tow net in Willapa Bay, Washington, where 20% of the intertidal area is utilized for shellfish aquaculture and thus is difficult to sample with conventional gear. Our goal was to compare fish use of relatively undisturbed habitats (open mudflat, seagrass, and channel habitats) with the use of nearby oyster culture habitat. Although many species showed significant temporal and spatial trends within the estuary, only Shiner Perch Cymatogaster aggregata exhibited a significant association with habitat. Juveniles of three salmonid species exhibited few associations with the low intertidal habitats over which they were captured or in the prey types they consumed there. Chinook Salmon O. tshawytscha, likely hatchery-released ocean-type fish, were the most common salmonid captured, and they utilized low intertidal areas throughout the summer as their mean size increased from 85 to 100 mm FL. Diets consumed by these larger juvenile Chinook Salmon were not associated with benthic habitat but instead consisted primarily of (1) insects from nearby marsh or terrestrial habitats and (2) planktonic prey, like decapod larvae and tunicate larvaceans. Juvenile Coho Salmon O. kisutch and Chum Salmon O. keta were captured earlier (April and May) and fed on a slightly different suite of prey taxa, which were also primarily pelagic rather than associated with the intertidal benthos. Our findings suggest that in this relatively shallow coastal estuary, the role of benthic habitat is not closely linked to its value as a source of food for large juvenile salmon out-migrants utilizing the low intertidal areas where aquaculture occurs

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions

Gaseous Dark Matter Detectors

Dark Matter detectors with directional sensitivity have the potential of yielding an unambiguous positive observation of WIMPs as well as discriminating between galactic Dark Matter halo models. In this article, we introduce the motivation for directional detectors, discuss the experimental techniques that make directional detection possible, and review the status of the experimental effort in this field.Comment: 19 pages, review on gaseous directional dark matter detectors submitted to New Journal of Physic