The Study of Pion Absorption on -4He at 355 MeV/C with LADS (Large Acceptance Detector System)

The medium and long range part of the nucleon-nucleon interaction can be described within the framework of pion exchange. In order to understand this fundamental interaction, it is therefore important to study the interaction of pions with nucleons and nuclei, which can either be elastic or inelastic scattering or absorption. Whereas the elastic and inelastic channels can be well described by different models, our understanding of pion absorption is still rather poor. There are still a lot of open questions, for instance on the strength of three and more nucleon absorption and the role of initial and final state interactions. In this thesis an experiment carried out at the Paul Scherrer Institut (PSI) in Villigen, Switzerland, to measure the cross section for the ppd final state from pion absorption on 4He is reported. The experiment was carried out during 1991 using the Large Acceptance Detector System (LADS) with a beam momentum of 355 MeV/c. LADS is a detector system which covers almost 4 π sr of the solid angle. Due to the complexity of the detector a Monte Carlo Program based on the CERN code Geant to simulate the response of the various components was written. To get a better understanding of the physics involved, different event generators modeled the various physics processes. The goal of the present treatise is to analyze the ppd final state and separate the different reactions leading to its formation. The data analyzed consisted of events from 4H as a calibration tool and events from 4He for this examination. It was found that three different mechanisms could be identified which would lead to this state. The first one is the two nucleon absorption with a recoiling spectator deuteron. In the second process, a deuteron is knocked out of the nucleus by the incoming pion which is then subsequently absorbed (Initial State Interaction or ISI). In the third reaction, one of the energetic outgoing protons from the two nucleon absorption picks up a neutron in a final state interaction (FSI). The cross sections for these three different processes were extracted and determined to be 5.6 mb, 4.8 mb and 1.9 mb respectively. The total integral of the cross section for the ppd final state is 12.3 mb

A Study of Alternative Catalysts and Analysis Methods for Biodiesel Production

This project aims to develop a cost efficient process for biodiesel production and can be divided in three main components: 1) production of biodiesel from a variety of fuel stocks using liquid morpholine as catalyst; 2) production of biodiesel using a homogeneous phase transfer catalyst; and 3) development of a method for using Infrared Spectroscopy (IR) to determine the extent of conversion of oil to biodiesel. The production of biodiesel from various fuel stocks in the presence of methanol using liquid morpholine as catalyst reduces the problems related to purification of the biodiesel since morpholine can be recovered by distillation. Furthermore the use of two homogeneous phase transfer catalyst, tetramethylammonium hydroxide (TMAH) and choline hydroxide (CH), was evaluated. The advantage of using these catalysts is that it allows for a better separation between the fuel and glycerin, thus additionally simplifying the purification procedure. Finally, this project endeavored to develop a way to use FT-IR to determine the purity of biodiesel samples obtained since FT-IR is faster and more readily available than the standard method of gas chromatographic analysis. For educational applications, a calibration curve was created by comparing data on the purity of biodiesel samples obtained from the GC-FID analysis to the ratio of the absorbances at 1197 cm-1 to 1166 cm-1 from the FT-IR spectrum. For field application, a similar method was developed using a portable IR spectrometer. The data collected gave a good linear fit for % purity of the samples versus absorbance ratio

Airport noise predicts song timing of European birds

Anthropogenic noise is of increasing concern to biologists and medical scientists. Its detrimental effects on human health have been well studied, with the high noise levels from air traffic being of particular concern. However, less is known about the effects of airport noise pollution on signal masking in wild animals. Here, we report a relationship between aircraft noise and two major features of the singing behavior of birds. We found that five of ten songbird species began singing significantly earlier in the morning in the vicinity of a major European airport than their conspecifics at a quieter control site. As birds at both sites started singing before the onset of air traffic in the morning, this suggests that the birds in the vicinity of the airport advanced their activity to gain more time for unimpaired singing before the massive plane noise set in. In addition, we found that during the day, chaffinches avoided singing during airplane takeoffs, but only when the noise exceeded a certain threshold, further suggesting that the massive noise caused by the airport can impair acoustic communication in birds. Overall, our study indicates that birds may be adjusting their mating signals and time budgets in response to aircraft noise

MuSiC: Identifying mutational significance in cancer genomes

Massively parallel sequencing technology and the associated rapidly decreasing sequencing costs have enabled systemic analyses of somatic mutations in large cohorts of cancer cases. Here we introduce a comprehensive mutational analysis pipeline that uses standardized sequence-based inputs along with multiple types of clinical data to establish correlations among mutation sites, affected genes and pathways, and to ultimately separate the commonly abundant passenger mutations from the truly significant events. In other words, we aim to determine the Mutational Significance in Cancer (MuSiC) for these large data sets. The integration of analytical operations in the MuSiC framework is widely applicable to a broad set of tumor types and offers the benefits of automation as well as standardization. Herein, we describe the computational structure and statistical underpinnings of the MuSiC pipeline and demonstrate its performance using 316 ovarian cancer samples from the TCGA ovarian cancer project. MuSiC correctly confirms many expected results, and identifies several potentially novel avenues for discovery

The hidden sterile neutrino and the (2+2) sum rule

We discuss oscillations of atmospheric and solar neutrinos into sterile neutrinos in the 2+2 scheme. A zeroth order sum rule requires equal probabilities for oscillation into nu_s and nu_tau in the solar+atmospheric data sample. Data does not favor this claim. Here we use scatter plots to assess corrections of the zeroth order sum rule when (i) the 4 x 4 neutrino mixing matrix assumes its full range of allowed values, and (ii) matter effects are included. We also introduce a related "product rule". We find that the sum rule is significantly relaxed, due to both the inclusion of the small mixing angles (which provide a short-baseline contribution) and to matter effects. The product rule is also dramatically altered. The observed relaxation of the sum rule weakens the case against the 2+2 model and the sterile neutrino. To invalidate the 2+2 model, a global fit to data with the small mixing angles included seems to be required.Comment: 43 pages, 11 figures (same as v2, accidental replacement

Rescue of DNA damage after constricted migration reveals a mechano-regulated threshold for cell cycle.

Migration through 3D constrictions can cause nuclear rupture and mislocalization of nuclear proteins, but damage to DNA remains uncertain, as does any effect on cell cycle. Here, myosin II inhibition rescues rupture and partially rescues the DNA damage marker γH2AX, but an apparent block in cell cycle appears unaffected. Co-overexpression of multiple DNA repair factors or antioxidant inhibition of break formation also exert partial effects, independently of rupture. Combined treatments completely rescue cell cycle suppression by DNA damage, revealing a sigmoidal dependence of cell cycle on excess DNA damage. Migration through custom-etched pores yields the same damage threshold, with ∼4-µm pores causing intermediate levels of both damage and cell cycle suppression. High curvature imposed rapidly by pores or probes or else by small micronuclei consistently associates nuclear rupture with dilution of stiff lamin-B filaments, loss of repair factors, and entry from cytoplasm of chromatin-binding cGAS (cyclic GMP-AMP synthase). The cell cycle block caused by constricted migration is nonetheless reversible, with a potential for DNA misrepair and genome variation

Compressed representation of a partially defined integer function over multiple arguments

In OLAP (OnLine Analitical Processing) data are analysed in an n-dimensional cube. The cube may be represented as a partially defined function over n arguments. Considering that often the function is not defined everywhere, we ask: is there a known way of representing the function or the points in which it is defined, in a more compact manner than the trivial one

Genome modeling system: A knowledge management platform for genomics

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms