Application of electron multiplying CCD technology in space instrumentation

Electron multiplying CCD (EMCCD) technology has found important initial applications in low light surveillance and photon starved scientific instrumentation. This paper discusses the attributes of the EMCCD which make it useful for certain space instruments, particularly those which are photon starved, and explores likely risks from the radiation expected in such instruments

Low noise charge injection in the CCD22

The inclusion of a charge injection structure on a charge coupled device (CCD) allows for the mitigation of charge transfer loss which can be caused by radiation induced charge trapping defects. Any traps present in the pixels of the CCD are filled by the injected charge as it is swept through the device and consequently, the charge transfer efficiency is improved in subsequently acquired images. To date, a number of different types of CCD have been manufactured featuring a variety of charge injection techniques. The e2v Technologies CCD22, used in the EPIC MOS focal plane instruments of XMM-Newton, is one such device and is the subject of this paper. A detailed understanding of charge injection operation and the use of charge injection to mitigate charge transfer losses resulting from radiation damage to CCDs will benefit a number of space projects planned for the future, including the ESA GAIA and X-ray Evolving Universe Spectrometry (XEUS) missions.The charge injection structure and mode of operation of the CCD22 are presented, followed by a detailed analysis of the uniformity and repeatability of the charge injection amplitude across the columns of the device. The effects of proton irradiation on the charge injection characteristics are also presented, in particular the effect of radiation induced bright pixels on the injected charge level

MOS CCDs for the wide field imager on the XEUS spacecraft

In recent years the XEUS mission concept has evolved and has been the subject of several industrial studies. The mission concept has now matured to the point that it could be proposed for a Phase A study and subsequent flight programme. The key feature of XEUS will be its X-ray optic with collecting area ~30-100x that of XMM. The mission is envisaged at an orbit around the L2 point in space, and is formed from two spacecraft; one for the mirrors, and the other for the focal plane detectors. With a focal length of 50m, the plate scale of the optic is 6.5x that of XMM, which using existing focal plane technology will reduce the effective field of view to a few arc minutes. Cryogenic instrumentation, with detector sizes of a few mm can only be used for narrow field studies of target objects, and a wide field instrument is under consideration using a DEPFET pixel array to image out to a diameter of 5 arcminutes, requiring an array of dimension 70mm. It is envisaged to extend this field of view possibly out to 15 arcminutes through the use of an outer detection ring comprised of MOS CCD

Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture

(ABRIDGED) We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations

The geography of recent genetic ancestry across Europe

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.Comment: Full size figures available from http://www.eve.ucdavis.edu/~plralph/research.html; or html version at http://ralphlab.usc.edu/ibd/ibd-paper/ibd-writeup.xhtm

Mixing patterns and the spread of close-contact infectious diseases

Surprisingly little is known regarding the human mixing patterns relevant to the spread of close-contact infections, such as measles, influenza and meningococcal disease. This study aims to estimate the number of partnerships that individuals make, their stability and the degree to which mixing is assortative with respect to age. We defined four levels of putative at-risk events from casual (physical contact without conversation) to intimate (contact of a sexual nature), and asked university student volunteers to record details on those they contacted at these levels on three separate days. We found that intimate contacts are stable over short time periods whereas there was no evidence of repeat casual contacts with the same individuals. The contacts were increasingly assortative as intimacy increased. Such information will aid the development and parameterisation of models of close contact diseases, and may have direct use in outbreak investigations

Variable Incidence of Spiroplasma Infections in Natural Populations of Drosophila Species

Spiroplasma is widespread as a heritable bacterial symbiont in insects and some other invertebrates, in which it sometimes acts as a male-killer and causes female-biased sex ratios in hosts. Besides Wolbachia, it is the only heritable bacterium known from Drosophila, having been found in 16 of over 200 Drosophila species screened, based on samples of one or few individuals per species. To assess the extent to which Spiroplasma infection varies within and among species of Drosophila, intensive sampling consisting of 50–281 individuals per species was conducted for natural populations of 19 Drosophila species. Infection rates varied among species and among populations of the same species, and 12 of 19 species tested negative for all individuals. Spiroplasma infection never was fixed, and the highest infection rates were 60% in certain populations of D. hydei and 85% in certain populations of D. mojavensis. In infected species, infection rates were similar for males and females, indicating that these Spiroplasma infections do not confer a strong male-killing effect. These findings suggest that Spiroplasma has other effects on hosts that allow it to persist, and that environmental or host variation affects transmission or persistence leading to differences among populations in infection frequencies

The strengths and limitations of routine staging before treatment with abdominal CT in colorectal cancer

<p>Abstract</p> <p>Background</p> <p>Advanced colorectal cancer (CRC), either locally advanced, metastasized (mCRC) or both, is present in a relevant proportion of patients. The chances on curation of advanced CRC are continuously improving with modern multi-modality treatment options. For incurable CRC the focus lies on palliation of symptoms, which is not necessarily a resection of the primary tumor. Both situations motivate adequate staging before treatment in CRC. This prospective observational study evaluates the outcomes after the introduction of routine staging with abdominal CT before treatment.</p> <p>Methods</p> <p>In a prospective observational study of 612 consecutive patients (2007-2009), the ability of abdominal CT to find liver metastases (LM), peritoneal carcinomatosis (PC) and T4 stage in colon cancer (CC) was analysed.</p> <p>Results</p> <p>Advanced CRC was present in 58% of patients, mCRC in 31%. The ability to find LM was excellent (99%), cT4 stage CC good (86%) and PC poor (33%). In the group of surgical patients with emergency presentations, the incidences of both mCRC (51%) and locally advanced colon cancer (LACC) (69%) were higher than in the elective group (20% and 26% respectively). Staging tended to be omitted more often in the emergency group (35% versus 12% in elective surgery).</p> <p>Conclusions</p> <p>The strengths of staging with abdominal CT are to find LM and LACC, however it fails in diagnosing PC. On grounds of the incidence of advanced CRC, staging is warranted in patients with emergency presentations as well.</p

Testicular cancer: a longitudinal pilot study on stress response symptoms and quality of life in couples before and after chemotherapy

Goals of work: The current study was designed to longitudinally examine stress response symptoms (SRS) and quality of life (QoL) in couples confronted with disseminated testicular cancer. The objectives were to examine couples' patterns of adjustment over time and possible differences in adjustment between the patient and his partner.Materials and methods: Couples completed the Impact of Event Scale and the QoL subscales physical functioning, social functioning, and mental health of the RAND-36 before chemotherapy (T1), after completion of chemotherapy (T2), and 1 year later (T3). Results: Before chemotherapy 26% of the patients and 50% of partners reported clinically elevated levels of SRS. Patients reported lower physical and social functioning at T2 compared to T1 and T3. Partners reported an improvement in social functioning over the year and no changes in physical functioning or mental health. No relationships between patients and partners' functioning were found. One year after diagnosis, QoL of patients and partners was similar to that of reference groups, and patients even reported better physical functioning than the reference group. SRS of patients and partners were negatively related at T1, and patients and partners' social functioning were positively related at T2. Conclusions: According to stress response levels, the period before the start of chemotherapy was most stressful for couples. Adjustment patterns differ between testicular cancer patients and their partners with patients reporting lowered QoL after completion of chemotherapy. QoL of couples returned to normal levels 1 year after diagnosis. The effect of disseminated testicular cancer on the QoL of patients and their partners seems to be temporary. A minority may need clinical attention for severe SRS