The Data Processing Pipeline for the Herschel-HIFI Instrument

The HIFI data processing pipeline was developed to systematically process diagnostic, calibration and astronomical observations taken with the HIFI science instrumentas part of the Herschel mission. The HIFI pipeline processed data from all HIFI observing modes within the Herschel automated processing environment, as well as, within an interactive environment. A common software framework was developed to best support the use cases required by the instrument teams and by the general astronomers. The HIFI pipeline was built on top of that and was designed with a high degree of modularity. This modular design provided the necessary flexibility and extensibility to deal with the complexity of batch-processing eighteen different observing modes, to support the astronomers in the interactive analysis and to cope with adjustments necessary to improve the pipeline and the quality of the end-products. This approach to the software development and data processing effort was arrived at by coalescing the lessons learned from similar research based projects with the understanding that a degree of foresight was required given the overall length of the project. In this article, both the successes and challenges of the HIFI software development process are presented. To support future similar projects and retain experience gained lessons learned are extracted.Comment: 18 pages, 5 figure

Predicting the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes

For many applications in microbial synthetic biology, optimizing a desired function requires careful tuning of the degree to which various genes are expressed. One challenge for predicting such effects or interpreting typical characterization experiments is that in bacteria such as E. coli, genome copy number varies widely across different phases and rates of growth, which also impacts how and when genes are expressed from different loci. While such phenomena are relatively well-understood at a mechanistic level, our quantitative understanding of such processes is essentially limited to ideal exponential growth. In contrast, common experimental phenomena such as growth on heterogeneous media, metabolic adaptation, and oxygen restriction all cause substantial deviations from ideal exponential growth, particularly as cultures approach the higher densities at which industrial biomanufacturing and even routine screening experiments are conducted. To meet the need for predicting and explaining how gene dosage impacts cellular functions outside of exponential growth, we here report a novel modeling strategy that leverages agent-based simulation and high performance computing to robustly predict the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes. We show that by feeding routine experimental data, such as optical density time series, into our heterogeneous multiphasic growth simulator, we can predict genomic DNA distributions over a range of nonexponential growth conditions. This modeling strategy provides an important advance in the ability of synthetic biologists to evaluate the role of genomic DNA content and heterogeneity in affecting the performance of existing or engineered microbial functions

Metacognitieve therapie voor de obsessieve-compulsieve stoornis

De obsessieve-compulsieve stoornis (OCS) is een veelvoorkomende en invaliderende stoornis. Cognitieve gedragstherapie (CGT) in de vorm van exposure met responspreventie (ERP) is de psychologische behandeling van eerste voorkeur. Ondanks de aangetoonde werkzaamheid van ERP is verbetering van de effectivitei

Individual scatterers as microscopic origin of equilibration between spin- polarized edge channels in the quantum Hall regime

The equilibration length between spin-polarized edge states in the Quantum Hall regime is measured as a function of a gate voltage applied to an electrode on top of the edge channels. Reproducible fluctuations in the coupling are observed and interpreted as a mesoscopic fingerprint of single spin-flip scatterers which are turned on and off. A model to analyze macroscopic edge state coupling in terms of individual scatterers is developed, and characteristic values for these scatterers in our samples are extracted. For all samples investigated, the distance between spin-flip scatterers lies between the Drude and the quantum scattering length.Comment: 4 pages, 2 figure

Changing spatial patterns and increasing rurality of HIV prevalence in the Democratic Republic of the Congo between 2007 and 2013

The Democratic Republic of the Congo (DRC) has one of the lowest HIV prevalence in sub-Saharan Africa, estimated at 1.1% [0.9-1.3] of adults aged 15-49 in 2013 (UNAIDS). Within the 2 million km2 country, however, there exists spatial variation in HIV prevalence, with the highest HIV prevalence observed in the large cities of Kinshasa and Lubumbashi. Globally, HIV is an increasingly rural disease, diffusing outwards from urban centers of high HIV prevalence to places where HIV was previously absent or present at very low levels. Utilizing data collected during Demographic and Health Surveillance (DHS) in 2007 and 2013 in the DRC, we sought to update the map of HIV prevalence in the DRC as well as to explore whether HIV in the DRC is an increasingly rural disease or remains confined to urban areas. Bayesian kriging and regression indicate that HIV prevalence in rural areas of the DRC is higher in 2013 than in 2007 and that increased distance to an urban area is no longer protective against HIV as it was in 2007. These findings suggest that HIV education, testing and prevention efforts need to diffuse from urban to rural areas just as HIV is doing

Characterization of a POROS\u3csup\u3eTM\u3c/sup\u3e-fumonisin B1 Affinity Column for Isolating Ceramide Synthase from Rat Liver

Fumonisin B1 is a mycotoxin produced by fungi of the genus Fusarium, common pathogens of corn and other grain plants. Toxic effects associated with fumonisin B1 include equine leukoencephalomacia, porcine pulmonary edema, rat renal carcinoma, and murine hepatocellular carcinoma. Increased risk for esophageal cancer in humans has been epidemiologically associated with consumption of corn contaminated with Fusarium, suggesting that fumonisin B1 may be involved. The biological effects of fumonisin B1 exposure result primarily from disruption of de novo sphingolipid biosynthesis via inhibition of ceramide synthase. Exposure of animals or cultured cells to fumonisin B1 results in the characteristic accumulation of sphinganine, a toxic sphingolipid intermediate, concomitant with depletion of essential complex sphingolipids. Ceramide synthase has not been purified to homogeniety and characterized. We prepared crude ceramide synthase from detergent-extracted rat liver homogenates using PEG-precipitation and cation exchange chromatography. Ceramide synthase activity was then sequestered, using fumonisin B1 covalently coupled to POROS-NH particles, and eluted selectively. The observed 119-fold enrichment in specific activity demonstrates the utility of fumonisin-POROS affinity chromatography in the purification of ceramide synthase

Difference Image Analysis of Galactic Microlensing I. Data Analysis

This is a preliminary report on the application of Difference Image Analysis (DIA) to galactic bulge images. The aim of this analysis is to increase the sensitivity to the detection of gravitational microlensing. We discuss how the DIA technique simplifies the process of discovering microlensing events by detecting only objects which have variable flux. We illustrate how the DIA technique is not limited to detection of so called ``pixel lensing'' events, but can also be used to improve photometry for classical microlensing events by removing the effects of blending. We will present a method whereby DIA can be used to reveal the true unblended colours, positions and light curves of microlensing events. We discuss the need for a technique to obtain the accurate microlensing time scales from blended sources, and present a possible solution to this problem using the existing HST colour magnitude diagrams of the galactic bulge and LMC. The use of such a solution with both classical and pixel microlensing searches is discussed. We show that one of the major causes of systematic noise in DIA is differential refraction. A technique for removing this systematic by effectively registering images to a common airmass is presented. Improvements to commonly used image differencing techniques are discussed.Comment: 18 pages, 8 figures, uses AAS LaTEX 4.0, To appear in Astrophysical Journa

Transient deSUMOylation of IRF2BP proteins controls early transcription in EGFR signaling

Molecular switches are essential modules in signaling networksand transcriptional reprogramming. Here, we describe a role forsmall ubiquitin-related modifier SUMO as a molecular switch inepidermal growth factor receptor (EGFR) signaling. Using quantita-tive mass spectrometry, we compare the endogenous SUMOproteomes of HeLa cells before and after EGF stimulation. Thereby,we identify a small group of transcriptional coregulators includingIRF2BP1, IRF2BP2, and IRF2BPL as novel players in EGFR signaling.Comparison of cells expressing wild type or SUMOylation-deficientIRF2BP1indicates that transient deSUMOylation of IRF2BP proteinsis important for appropriate expression of immediate early genesincludingdual specificity phosphatase1(DUSP1, MKP-1) and thetranscription factor ATF3. We find that IRF2BP1is a repressor,whose transient deSUMOylation on the DUSP1promoter allows—and whose timely reSUMOylation restricts—DUSP1transcription.Our work thus provides a paradigm how comparative SUMOproteome analyses serve to reveal novel regulators in signal trans-duction and transcription