Is classical reality completely deterministic?

The concept of determinism for a classical system is interpreted as the requirement that the solution to the Cauchy problem for the equations of motion governing this system be unique. This requirement is generally assumed to hold for all autonomous classical systems. We give counterexamples of this view. Our analysis of classical electrodynamics in a world with one temporal and one spatial dimension shows that the solution to the Cauchy problem with the initial conditions of a particular type is not unique. Therefore, random behavior of closed classical systems is indeed possible. This finding provides a qualitative explanation of how classical strings can split. We propose a modified path integral formulation of classical mechanics to include indeterministic systems.Comment: Replace the paper with a revised versio

Exactly solvable model of superstring in Ramond-Ramond plane wave background

We describe in detail the solution of type IIB superstring theory in the maximally supersymmetric plane-wave background with constant null Ramond-Ramond 5-form field strength. The corresponding light-cone Green-Schwarz action found in hep-th/0112044 is quadratic in both bosonic and fermionic coordinates. We find the spectrum of the light-cone Hamiltonian and the string representation of the supersymmetry algebra. The superstring Hamiltonian has a ``harmonic-oscillator'' form in both the string-oscillator and the zero-mode parts and thus has discrete spectrum in all 8 transverse directions. We analyze the structure of the zero-mode sector of the theory, establishing the precise correspondence between the lowest-lying ``massless'' string states and the type IIB supergravity fluctuation modes in the plane-wave background. The zero-mode spectrum has certain similarity to the supergravity spectrum in AdS_5 x S^5 of which the plane-wave background is a special limit. We also compare the plane-wave string spectrum with expected form of the light-cone gauge spectrum of superstring in AdS_5 x S^5.Comment: 33 pages, latex. v4: minor sign corrections in (1.5) and (3.62), to appear in PR

Exact diagonalization of the generalized supersymmetric t-J model with boundaries

We study the generalized supersymmetric $t-J$ model with boundaries in three different gradings: FFB, BFF and FBF. Starting from the trigonometric R-matrix, and in the framework of the graded quantum inverse scattering method (QISM), we solve the eigenvalue problems for the supersymmetric $t-J$ model. A detailed calculations are presented to obtain the eigenvalues and Bethe ansatz equations of the supersymmetric $t-J$ model with boundaries in three different backgrounds.Comment: Latex file, 32 page

Deep inelastic scattering of baryons in a modified soft wall model

We calculate the structure functions for unpolarized deep inelastic scattering of baryons using an AdS/QCD soft wall model that considers a dressed mass for the bulk fermionic fields. Considering the regime of large Bjorken parameter x, we compare the results for the proton structure function $F_2$ with experimental results.Comment: We improved the comparison with experimental data and included more references, version to appear in EPJ

The Bethe-Ansatz for N=4 Super Yang-Mills

We derive the one loop mixing matrix for anomalous dimensions in N=4 Super Yang-Mills. We show that this matrix can be identified with the Hamiltonian of an integrable SO(6) spin chain with vector sites. We then use the Bethe ansatz to find a recipe for computing anomalous dimensions for a wide range of operators. We give exact results for BMN operators with two impurities and results up to and including first order 1/J corrections for BMN operators with many impurities. We then use a result of Reshetikhin's to find the exact one-loop anomalous dimension for an SO(6) singlet in the limit of large bare dimension. We also show that this last anomalous dimension is proportional to the square root of the string level in the weak coupling limit.Comment: 35 pages, 3 figures, LaTeX; v2 references added, typos corrected, \Lambda fixed; v3 expanded discussion of higher loops in conclusion, matches published versio

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.

Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans – anteaters, sloths, and armadillos – have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with 24 domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, ten anteaters, and six sloths. Our dataset includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data-paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the south of the USA, Mexico, and Caribbean countries at the northern portion of the Neotropics, to its austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n=5,941), and Cyclopes sp. has the fewest (n=240). The armadillo species with the most data is Dasypus novemcinctus (n=11,588), and the least recorded for Calyptophractus retusus (n=33). With regards to sloth species, Bradypus variegatus has the most records (n=962), and Bradypus pygmaeus has the fewest (n=12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other datasets of Neotropical Series which will become available very soon (i.e. Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans dataset

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR