Clock and Trigger Synchronization between Several Chassis of Digital Data Acquisition Modules

In applications with segmented high purity Ge detectors or other detector arrays with tens or hundreds of channels, where the high development cost and limited flexibility of application specific integrated circuits outweigh their benefits of low power and small size, the readout electronics typically consist of multi-channel data acquisition modules in a common chassis for power, clock and trigger distribution, and data readout. As arrays become larger and reach several hundred channels, the readout electronics have to be divided over several chassis, but still must maintain precise synchronization of clocks and trigger signals across all channels. This division becomes necessary not only because of limits given by the instrumentation standards on module size and chassis slot numbers, but also because data readout times increase when more modules share the same data bus and because power requirements approach the limits of readily available power supplies. In this paper, we present a method for distributing clocks and triggers between 4 PXI chassis containing DGF Pixie-16 modules with up to 226 acquisition channels per chassis in a data acquisition system intended to instrument the over 600 channels of the SeGA detector array at the National Superconducting Cyclotron Laboratory. Our solution is designed to achieve synchronous acquisition of detector waveforms from all channels with a jitter of less then 1 ns, and can be extended to a larger number of chassis if desired.Comment: CAARI 200

SkinSafe: Comparing Staphylococcus aureus Growth Across Liner Types in Kenya

The interface between an amputee’s residual limb and prosthetic liner is at risk for high levels of bacterial growth which can lead to infection. Silicone liners have the advantage of patient comfort, but they may have a sealing effect that could exacerbate bacterial growth, which is particularly a concern in places lacking clean water such as Kijabe, Kenya. To investigate this concern, the SkinSafe team has conducted a prosthetic liner study using a bacterial skin model which suspends a liner and a layer of agar above a self-regulating heat and water source to capture the dynamic behavior of the skin–liner interface. Staphylococcus aureus was grown on this model using three different liners: the Ossur Iceross silicone liner, the Namaste silicone liner, and the sock–EVA liner. Final growth concentrations will be compared between the three liner types to determine whether silicone liners require additional hygiene protocols for use in Kenya. Funding for this work provided by The Collaboratory for Strategic Partnerships and Applied Research.https://mosaic.messiah.edu/engr2022/1015/thumbnail.jp

An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations

We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination

Measuring Black Hole Spin using X-ray Reflection Spectroscopy

I review the current status of X-ray reflection (a.k.a. broad iron line) based black hole spin measurements. This is a powerful technique that allows us to measure robust black hole spins across the mass range, from the stellar-mass black holes in X-ray binaries to the supermassive black holes in active galactic nuclei. After describing the basic assumptions of this approach, I lay out the detailed methodology focusing on "best practices" that have been found necessary to obtain robust results. Reflecting my own biases, this review is slanted towards a discussion of supermassive black hole (SMBH) spin in active galactic nuclei (AGN). Pulling together all of the available XMM-Newton and Suzaku results from the literature that satisfy objective quality control criteria, it is clear that a large fraction of SMBHs are rapidly-spinning, although there are tentative hints of a more slowly spinning population at high (M>5*10^7Msun) and low (M<2*10^6Msun) mass. I also engage in a brief review of the spins of stellar-mass black holes in X-ray binaries. In general, reflection-based and continuum-fitting based spin measures are in agreement, although there remain two objects (GROJ1655-40 and 4U1543-475) for which that is not true. I end this review by discussing the exciting frontier of relativistic reverberation, particularly the discovery of broad iron line reverberation in XMM-Newton data for the Seyfert galaxies NGC4151, NGC7314 and MCG-5-23-16. As well as confirming the basic paradigm of relativistic disk reflection, this detection of reverberation demonstrates that future large-area X-ray observatories such as LOFT will make tremendous progress in studies of strong gravity using relativistic reverberation in AGN.Comment: 19 pages. To appear in proceedings of the ISSI-Bern workshop on "The Physics of Accretion onto Black Holes" (8-12 Oct 2012). Revised version adds a missing source to Table 1 and Fig.6 (IRAS13224-3809) and corrects the referencing of the discovery of soft lags in 1H0707-495 (which were in fact first reported in Fabian et al. 2009

Integrative analyses identify modulators of response to neoadjuvant aromatase inhibitors in patients with early breast cancer

Introduction Aromatase inhibitors (AIs) are a vital component of estrogen receptor positive (ER+) breast cancer treatment. De novo and acquired resistance, however, is common. The aims of this study were to relate patterns of copy number aberrations to molecular and proliferative response to AIs, to study differences in the patterns of copy number aberrations between breast cancer samples pre- and post-AI neoadjuvant therapy, and to identify putative biomarkers for resistance to neoadjuvant AI therapy using an integrative analysis approach. Methods Samples from 84 patients derived from two neoadjuvant AI therapy trials were subjected to copy number profiling by microarray-based comparative genomic hybridisation (aCGH, n = 84), gene expression profiling (n = 47), matched pre- and post-AI aCGH (n = 19 pairs) and Ki67-based AI-response analysis (n = 39). Results Integrative analysis of these datasets identified a set of nine genes that, when amplified, were associated with a poor response to AIs, and were significantly overexpressed when amplified, including CHKA, LRP5 and SAPS3. Functional validation in vitro, using cell lines with and without amplification of these genes (SUM44, MDA-MB134-VI, T47D and MCF7) and a model of acquired AI-resistance (MCF7-LTED) identified CHKA as a gene that when amplified modulates estrogen receptor (ER)-driven proliferation, ER/estrogen response element (ERE) transactivation, expression of ER-regulated genes and phosphorylation of V-AKT murine thymoma viral oncogene homolog 1 (AKT1). Conclusions These data provide a rationale for investigation of the role of CHKA in further models of de novo and acquired resistance to AIs, and provide proof of concept that integrative genomic analyses can identify biologically relevant modulators of AI response

Over-expression of severe acute respiratory syndrome coronavirus 3b protein induces both apoptosis and necrosis in Vero E6 cells

The genome of the severe acute respiratory syndrome coronavirus encodes for eight accessory viral proteins with no known homologues in other coronaviruses. One of these is the 3b protein, which is encoded by the second open reading frame in subgenomic RNA 3 and contains 154 amino acids. Here, a detailed time-course study was performed to compare the apoptosis and necrosis profiles induced by full-length 3b, a 3b mutant that was deleted by 30 amino acids from the C terminus (3b 124-154) and the classical apoptosis inducer, Bax. Our results showed that Vero E6 cells transfected with a construct for expressing 3b underwent necrosis as early as 6 h after transfection and underwent simultaneous necrosis and apoptosis at later time-points. At all the time-points analysed, the apoptosis induced by the expression of 3b was less than the level induced by Bax but the level of necrosis was comparable. The 3b 124-154 mutant behaves in a similar manner indicating that the localization of the 3b protein does not seems to be important for the cell-death pathways since full-length 3b is localized predominantly to the nucleolus, while the mutant is found to be concentrated in the peri-nuclear regions. To our knowledge, this is the first report of the induction of necrosis by a SARS-CoV protein.IS

The influence of spin on jet power in neutron star X-ray binaries

We investigate the role of the compact object in the production of jets from neutron star X-ray binaries. The goal is to quantify the effect of the neutron star spin, if any, in powering the jet. We compile all the available measures or estimates of the neutron star spin frequency in jet-detected neutron star X-ray binaries. We use as an estimate of the ranking jet power for each source, the normalisation of the power law which fits the X-ray/radio and X-ray/infrared luminosity correlations L_(radio/IR) proportional to L_(X)^(Gamma) (using infrared data for which there is evidence for jet emission). We find a possible relation between spin frequency and jet power (Spearman rank 97%), when fitting the X-ray/radio luminosity correlation using a power law with slope 1.4; Gamma=1.4 is observed in 4U 1728-34 and is predicted for a radiatively efficient disc and a total jet power proportional to the mass accretion rate. If we use a slope of 0.6, as observed in Aql X-1, no significant relation is found. An indication for a similar positive correlation is also found for accreting millisecond X-ray pulsars (Spearman rank 92%), if we fit the X-ray/infrared luminosity correlation using a power law with slope 1.4. While our use of the normalisation of the luminosity correlations as a measure of the ranking jet power is subject to large uncertainties, no better proxy for the jet power is available. However, we urge caution in over-interpreting the spin-jet power correlations, particularly given the strong dependence of our result on the (highly uncertain) assumed power law index of the luminosity correlations. We discuss the results in the framework of current models for jet formation in black holes and young stellar objects and speculate on possible different jet production mechanisms for neutron stars depending on the accretion mode.Comment: Accepted for publication in MNRA

Radiotherapy for marginally resected, unresectable or recurrent giant cell tumor of the bone: a rare cancer network study

The role of radiotherapy for local control of marginally resected, unresectable, and recurrent giant cell tumors of bone (GCToB) has not been well defined. The number of patients affected by this rare disease is low. We present a series of 58 patients with biopsy proven GCToB who were treated with radiation therapy. A retrospective review of the role of radiotherapy in the treatment of GCToB was conducted in participating institutions of the Rare Cancer Network. Eligibility criteria consisted of the use of radiotherapy for marginally resected, unresectable, and recurrent GCToB. Fifty-eight patients with biopsy proven GCToB were analyzed from 9 participating North American and European institutions. Forty-five patients had a primary tumor and 13 patients had a recurrent tumor. Median radiation dose was 50 Gy in a median of 25 fractions. Indication for radiation therapy was marginal resection in 33 patients, unresectable tumor in 13 patients, recurrence in 9 patients and palliation in 2 patients. Median tumor size was 7.0 cm. A significant proportion of the tumors involved critical structures. Median follow-up was 8.0 years. Five year local control was 85% . Of the 7 local failures, 3 were treated successfully with salvage surgery. All patients who received palliation achieved symptom relief. Five year overall survival was 94%. None of the patients experienced grade 3 or higher acute toxicity. This study reports a large published experience in the treatment of GCToB with radiotherapy. Radiotherapy can provide excellent local control for incompletely resected, unresectable or recurrent GCToB with acceptable morbidity

Population Structure Shapes Copy Number Variation in Malaria Parasites.

If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen