Heap analysis in the presence of collection libraries

Memory analysis techniques have become sophisticated enough to model, with a high degree of accuracy, the manipulation of simple memory structures (finite structures, single/double linked lists and trees). However, modern programming languages provide extensive library support including a wide range of generic collection objects that make use of complex internal data structures. While these data structures ensure that the collections are efficient, often these representations cannot be effectively modeled by existing methods (either due to excessive analysis runtime or due to the inability to represent the required information). This paper presents a method to represent collections using an abstraction of their semantics. The construction of the abstract semantics for the collection objects is done in a manner that allows individual elements in the collections to be identified. Our construction also supports iterators over the collections and is able to model the position of the iterators with respect to the elements in the collection. By ordering the contents of the collection based on the iterator position, the model can represent a notion of progress when iteratively manipulating the contents of a collection. These features allow strong updates to the individual elements in the collection as well as strong updates over the collections themselves.

Analysis of different uncertainty activation cross section data libraries for LWR, ADS and DEMO neutron spectra

This work is aimed to present the main differences of nuclear data uncertainties among three different nuclear data libraries: EAF-2007, EAF-2010 and SCALE-6.0, under different neutron spectra: LWR, ADS and DEMO (fusion). To take into account the neutron spectrum, the uncertainty data are collapsed to onegroup. That is a simple way to see the differences among libraries for one application. Also, the neutron spectrum effect on different applications can be observed. These comparisons are presented only for (n,fission), (n,gamma) and (n,p) reactions, for the main transuranic isotopes (234,235,236,238U, 237Np, 238,239,240,241Pu, 241,242m,243Am, 242,243,244,245,246,247,248Cm, 249Bk, 249,250,251,252Cf). But also general comparisons among libraries are presented taking into account all included isotopes. In other works, target accuracies are presented for nuclear data uncertainties; here, these targets are compared with uncertainties on the above libraries. The main results of these comparisons are that EAF-2010 has reduced their uncertainties for many isotopes from EAF-2007 for (n,gamma) and (n,fission) but not for (n,p); SCALE-6.0 gives lower uncertainties for (n,fission) reactions for ADS and PWR applications, but gives higher uncertainties for (n,p) reactions in all applications. For the (n,gamma) reaction, the amount of isotopes which have higher uncertainties is quite similar to the amount of isotopes which have lower uncertainties when SCALE-6.0 and EAF-2010 are compared. When the effect of neutron spectra is analysed, the ADS neutron spectrum obtained the highest uncertainties for (n,gamma) and (n,fission) reactions of all libraries.

Testing JEFF-3.1.1 and ENDF/B-VII.1 Decay and Fission Yield Nuclear Data Libraries with Fission Pulse Neutron Emission and Decay Heat Experiments

The aim of this work is to test the present status of Evaluated Nuclear Decay and Fission Yield Data Libraries to predict decay heat and delayed neutron emission rate, average neutron energy and neutron delayed spectra after a neutron fission pulse. Calculations are performed with JEFF-3.1.1 and ENDF/B-VII.1, and these are compared with experimental values. An uncertainty propagation assessment of the current nuclear data uncertainties is performed.

Impact of Nuclear Data Uncertainties on Advanced Fuel Cycles and Their Irradiated Fuel - A comparison between Libraries

The uncertainties on the isotopic composition throughout the burnup due to the nuclear data uncertainties are analysed. The different sources of uncertainties: decay data, fission yield and cross sections; are propagated individually, and their effect assessed. Two applications are studied: EFIT (an ADS-like reactor) and ESFR (Sodium Fast Reactor). The impact of the uncertainties on cross sections provided by the EAF-2010, SCALE6.1 and COMMARA-2.0 libraries are compared. These Uncertainty Quantification (UQ) studies have been carried out with a Monte Carlo sampling approach implemented in the depletion/activation code ACAB. Such implementation has been improved to overcome depletion/activation problems with variations of the neutron spectrum.

Digital libraries for the preservation of research methods and associated artifacts

New digital artifacts are emerging in data-intensive science. For example, scientific workflows are executable descriptions of scientific procedures that define the sequence of computational steps in an automated data analysis, supporting reproducible research and the sharing and replication of best-practice and know-how through reuse. Workflows are specified at design time and interpreted through their execution in a variety of situations, environments, and domains. Hence it is essential to preserve both their static and dynamic aspects, along with the research context in which they are used. To achieve this, we propose the use of multidimensional digital objects (Research Objects) that aggregate the resources used and/or produced in scientific investigations, including workflow models, provenance of their executions, and links to the relevant associated resources, along with the provision of technological support for their preservation and efficient retrieval and reuse. In this direction, we specified a software architecture for the design and implementation of a Research Object preservation system, and realized this architecture with a set of services and clients, drawing together practices in digital libraries, preservation systems, workflow management, social networking and Semantic Web technologies. In this paper, we describe the backbone system of this realization, a digital library system built on top of dLibra.

Thermal Scattering Libraries Processing (F4E, Task 6.2)

Presentación del trabajo realizado en el marco del proyecto F4E, sobre el procesamiento de librerías de dispersión térmica de neutrones en formato ACE para su uso con el código MCNP. Se presentan tanto los métodos y procedimientos empleados, como los resultados y diferencias entre las distintas fuentes de datos.

Libraries Transforming Communities: The Value in an Academic Library Community at Lincoln University

Inman E. Page Library is coined as an, “Information Mall.” It houses special collections, archives, general reference services, computers, artistic programming, technological resources and space for different types of events. It is a modern academic library in the 21st century that was built on a legacy of scholarly opportunities for Lincoln University students, faculty, and our community in Jefferson City, MO and surrounding cities. The value that needs to be placed on this library is that it is an institution within an institution and should be given top priority as it pertains to continued funding, faculty support, and a place of higher learning that has a library etiquette. As well as, students need to understand the importance of how a library will affect their academic careers.

Creating Information Literacy Toolkits For HBCU Libraries

Information literacy is the set of research skills needed to access, retrieve, and analyze information. By creating an information literacy plan and an online toolkit that the entire campus uses for research purposes, faculty and students will be equipped with the necessary tools to become better researchers, understand the importance of citing information and the significance of searching for peer-reviewed articles.

A novel glutamine–RNA interaction identified by screening libraries in mammalian cells

The arginine-rich motif provides a versatile framework for RNA recognition in which few amino acids other than arginine are needed to mediate specific binding. Using a mammalian screening system based on transcriptional activation by HIV Tat, we identified novel arginine-rich peptides from combinatorial libraries that bind tightly to the Rev response element of HIV. Remarkably, a single glutamine, but not asparagine, within a stretch of polyarginine can mediate high-affinity binding. These results, together with the structure of a Rev peptide-Rev response element complex, suggest that the carboxamide groups of glutamine or asparagine are well-suited to hydrogen bond to G-A base pairs and begin to establish an RNA recognition code for the arginine-rich motif. The screening approach may provide a relatively general method for screening expression libraries in mammalian cells.

Recognition principle of the TAP transporter disclosed by combinatorial peptide libraries

Transport of peptides across the membrane of the endoplasmic reticulum for assembly with MHC class I molecules is an essential step in antigen presentation to cytotoxic T cells. This task is performed by the major histocompatibility complex-encoded transporter associated with antigen processing (TAP). Using a combinatorial approach we have analyzed the substrate specificity of human TAP at high resolution and in the absence of any given sequence context, revealing the contribution of each peptide residue in stabilizing binding to TAP. Human TAP was found to be highly selective with peptide affinities covering at least three orders of magnitude. Interestingly, the selectivity is not equally distributed over the substrate. Only the N-terminal three positions and the C-terminal residue are critical, whereas effects from other peptide positions are negligible. A major influence from the peptide backbone was uncovered by peptide scans and libraries containing d amino acids. Again, independent of peptide length, critical positions were clustered near the peptide termini. These approaches demonstrate that human TAP is selective, with residues determining the affinity located in distinct regions, and point to the role of the peptide backbone in binding to TAP. This binding mode of TAP has implications in an optimized repertoire selection and in a coevolution with the major histocompatibility complex/T cell receptor complex.

Comparison of fusion phage libraries displaying VH or single-chain Fv antibody fragments derived from the antibody repertoire of a vaccinated melanoma patient as a source of melanoma-specific targeting molecules

A single-chain Fv (scFv) fusion phage library derived from random combinations of VH and VL (variable heavy and light chains) domains in the antibody repertoire of a vaccinated melanoma patient was previously used to isolate clones that bind specifically to melanoma cells. An unexpected finding was that one of the clones encoded a truncated scFv molecule with most of the VL domain deleted, indicating that a VH domain alone can exhibit tumor-specific binding. In this report a VH fusion phage library containing VH domains unassociated with VL domains was compared with a scFv fusion phage library as a source of melanoma-specific clones; both libraries contained the same VH domains from the vaccinated melanoma patient. The results demonstrate that the clones can be isolated from both libraries, and that both libraries should be used to optimize the chance of isolating clones binding to different epitopes. Although this strategy has been tested only for melanoma, it is also applicable to other cancers. Because of their small size, human origin and specificity for cell surface tumor antigens, the VH and scFv molecules have significant advantages as tumor-targeting molecules for diagnostic and therapeutic procedures and can also serve as probes for identifying the cognate tumor antigens.

The identification of CD4+ T cell epitopes with dedicated synthetic peptide libraries

For a large number of T cell-mediated immunopathologies, the disease-related antigens are not yet identified. Identification of T cell epitopes is of crucial importance for the development of immune-intervention strategies. We show that CD4+ T cell epitopes can be defined by using a new system for synthesis and screening of synthetic peptide libraries. These libraries are designed to bind to the HLA class II restriction molecule of the CD4+ T cell clone of interest. The screening is based on three selection rounds using partial release of 14-mer peptides from synthesis beads and subsequent sequencing of the remaining peptide attached to the bead. With this approach, two peptides were identified that stimulate the β cell-reactive CD4+ T cell clone 1c10, which was isolated from a newly diagnosed insulin-dependent diabetes mellitus patient. After performing amino acid-substitution studies and protein database searches, a Haemophilus influenzae TonB-derived peptide was identified that stimulates clone 1c10. The relevance of this finding for the pathogenesis of insulin-dependent diabetes mellitus is currently under investigation. We conclude that this system is capable of determining epitopes for (autoreactive) CD4+ T cell clones with previously unknown peptide specificity. This offers the possibility to define (auto)antigens by searching protein databases and/or to induce tolerance by using the peptide sequences identified. In addition the peptides might be used as leads to develop T cell receptor antagonists or anergy-inducing compounds.

Synthesis and screening of small molecule libraries active in binding to DNA

Five synthetic combinatorial libraries of 2,080 components each were screened as mixtures for inhibition of DNA binding to two transcription factors. Rapid, solution-phase synthesis coupled to a gel-shift assay led to the identification of two compounds active at a 5- to 10-μM concentration level. The likely mode of inhibition is intercalation between DNA base pairs. The efficient deconvolution through sublibrary synthesis augurs well for the use of large mixtures of small, nonpeptide molecules in biological screens.

Identification of differentially expressed mRNA in prokaryotic organisms by customized amplification libraries (DECAL): The effect of isoniazid on gene expression in Mycobacterium tuberculosis

Understanding the effects of the external environment on bacterial gene expression can provide valuable insights into an array of cellular mechanisms including pathogenesis, drug resistance, and, in the case of Mycobacterium tuberculosis, latency. Because of the absence of poly(A)+ mRNA in prokaryotic organisms, studies of differential gene expression currently must be performed either with large amounts of total RNA or rely on amplification techniques that can alter the proportional representation of individual mRNA sequences. We have developed an approach to study differences in bacterial mRNA expression that enables amplification by the PCR of a complex mixture of cDNA sequences in a reproducible manner that obviates the confounding effects of selected highly expressed sequences, e.g., ribosomal RNA. Differential expression using customized amplification libraries (DECAL) uses a library of amplifiable genomic sequences to convert total cellular RNA into an amplified probe for gene expression screens. DECAL can detect 4-fold differences in the mRNA levels of rare sequences and can be performed on as little as 10 ng of total RNA. DECAL was used to investigate the in vitro effect of the antibiotic isoniazid on M. tuberculosis, and three previously uncharacterized isoniazid-induced genes, iniA, iniB, and iniC, were identified. The iniB gene has homology to cell wall proteins, and iniA contains a phosphopantetheine attachment site motif suggestive of an acyl carrier protein. The iniA gene is also induced by the antibiotic ethambutol, an agent that inhibits cell wall biosynthesis by a mechanism that is distinct from isoniazid. The DECAL method offers a powerful new tool for the study of differential gene expression.

Continuous and lurching traveling pulses in neuronal networks with delay and spatially decaying connectivity

Propagation of discharges in cortical and thalamic systems, which is used as a probe for examining network circuitry, is studied by constructing a one-dimensional model of integrate-and-fire neurons that are coupled by excitatory synapses with delay. Each neuron fires only one spike. The velocity and stability of propagating continuous pulses are calculated analytically. Above a certain critical value of the constant delay, these pulses lose stability. Instead, lurching pulses propagate with discontinuous and periodic spatio-temporal characteristics. The parameter regime for which lurching occurs is strongly affected by the footprint (connectivity) shape; bistability may occur with a square footprint shape but not with an exponential footprint shape. For strong synaptic coupling, the velocity of both continuous and lurching pulses increases logarithmically with the synaptic coupling strength gsyn for an exponential footprint shape, and it is bounded for a step footprint shape. We conclude that the differences in velocity and shape between the front of thalamic spindle waves in vitro and cortical paroxysmal discharges stem from their different effective delay; in thalamic networks, large effective delay between inhibitory neurons arises from their effective interaction via the excitatory cells which display postinhibitory rebound.