GiViP: A Visual Profiler for Distributed Graph Processing Systems

Analyzing large-scale graphs provides valuable insights in different application scenarios. While many graph processing systems working on top of distributed infrastructures have been proposed to deal with big graphs, the tasks of profiling and debugging their massive computations remain time consuming and error-prone. This paper presents GiViP, a visual profiler for distributed graph processing systems based on a Pregel-like computation model. GiViP captures the huge amount of messages exchanged throughout a computation and provides an interactive user interface for the visual analysis of the collected data. We show how to take advantage of GiViP to detect anomalies related to the computation and to the infrastructure, such as slow computing units and anomalous message patterns.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

A time-domain control signal detection technique for OFDM

Transmission of system-critical control information plays a key role in efficient management of limited wireless network resources and successful reception of payload data information. This paper uses an orthogonal frequency division multiplexing (OFDM) architecture to investigate the detection performance of a time-domain approach used to detect deterministic control signalling information. It considers a type of control information chosen from a finite set of information, which is known at both transmitting and receiving wireless terminals. Unlike the maximum likelihood (ML) estimation method, which is often used, the time-domain detection technique requires no channel estimation and no pilots as it uses a form of time-domain correlation as the means of detection. Results show that when compared with the ML method, the time-domain approach improves detection performance even in the presence of synchronisation error caused by carrier frequency offset

From z>6 to z~2: Unearthing Galaxies at the Edge of the Dark Ages

Galaxies undergoing formation and evolution can now be observed over a time baseline of some 12 Gyr. An inherent difficulty with high-redshift observations is that the objects are very faint and the best resolution (HST) is only ~0.5 kpc. Such studies thereby combine in a highly synergistic way with the great detail that can be obtained for nearby galaxies. 3 new developments are highlighted. First is the derivation of stellar masses for galaxies from SEDs using HST and now Spitzer data, and dynamical masses from both sub-mm observations of CO lines and near-IR observations of optical lines like Halpha. A major step has been taken with evidence that points to the z~2-3 LBGs having masses that are a few x 10^10 Msolar. Second is the discovery of a population of evolved red galaxies at z~2-3 which appear to be the progenitors of the more massive early-type galaxies of today, with dynamical masses around a few x 10^11 Msolar. Third are the remarkable advances that have occurred in characterizing dropout galaxies to z~6 and beyond, < 1 Gyr from recombination. The HST ACS has played a key role here, with the dropout technique being applied to i & z images in several deep ACS fields, yielding large samples of these objects. This has allowed a detailed determination of their properties and meaningful comparisons against lower-z samples. The use of cloning techniques has overcome many of the strong selection biases affecting the study of these objects. A clear trend of size with redshift has been identified, and its impact on the luminosity density and SFR estimated. There is a significant though modest decrease in the SFR from z~2.5 to z~6. The latest data also allow for the first robust determination of the LF at z~6. Finally, the latest UDF ACS and NICMOS data has resulted in the detection of some galaxies at z~7-8.Comment: 18 pages, 8 figures. To appear in Penetrating Bars through Masks of Cosmic Dust: The Hubble Tuning Fork Strikes a New Note, eds. D. Block, K. Freeman, R. Groess, I. Puerari, & E.K. Block (Dordrecht: Kluwer), in pres

Evaluating methane inventories by isotopic analysis in the London region

A thorough understanding of methane sources is necessary to accomplish methane reduction targets. Urban environments, where a large variety of methane sources coexist, are one of the most complex areas to investigate. Methane sources are characterised by specific δ13C-CH4 signatures, so high precision stable isotope analysis of atmospheric methane can be used to give a better understanding of urban sources and their partition in a source mix. Diurnal measurements of methane and carbon dioxide mole fraction, and isotopic values at King’s College London, enabled assessment of the isotopic signal of the source mix in central London. Surveys with a mobile measurement system in the London region were also carried out for detection of methane plumes at near ground level, in order to evaluate the spatial allocation of sources suggested by the inventories. The measured isotopic signal in central London (−45.7 ±0.5‰) was more than 2‰ higher than the isotopic value calculated using emission inventories and updated δ13C-CH4 signatures. Besides, during the mobile surveys, many gas leaks were identified that are not included in the inventories. This suggests that a revision of the source distribution given by the emission inventories is needed

Catastrophizing mediates the relationship between the personal belief in a just world and pain outcomes among chronic pain support group attendees

Health-related research suggests the belief in a just world can act as a personal resource that protects against the adverse effects of pain and illness. However, currently, little is known about how this belief, particularly in relation to one’s own life, might influence pain. Consistent with the suggestions of previous research, the present study undertook a secondary data analysis to investigate pain catastrophizing as a mediator of the relationship between the personal just world belief and chronic pain outcomes in a sample of chronic pain support group attendees. Partially supporting the hypotheses, catastrophizing was negatively correlated with the personal just world belief and mediated the relationship between this belief and pain and disability, but not distress. Suggestions for future research and intervention development are made

Onchocerciasis transmission in Ghana: biting and parous rates of host-seeking sibling species of the Simulium damnosum complex

Background: Ghana is renowned for its sibling species diversity of the Simulium damnosum complex, vectors of Onchocerca volvulus. Detailed entomological knowledge becomes a priority as onchocerciasis control policy has shifted from morbidity reduction to elimination of infection. To date, understanding of transmission dynamics of O. volvulus has been mainly based on S. damnosum sensu stricto (s.s.) data. We aim to elucidate bionomic features of vector species of importance for onchocerciasis elimination efforts. Methods: We collected S. damnosum sensu lato from seven villages in four Ghanaian regions between 2009 and 2011, using standard vector collection, and human- and cattle-baited tents. Taxa were identified using morphological and molecular techniques. Monthly biting rates (MBR), parous rates and monthly parous biting rates (MPBR) are reported by locality, season, trapping method and hour of collection for each species. Results: S. damnosum s.s./S. sirbanum were collected at Asubende and Agborlekame, both savannah villages. A range of species was caught in the Volta region (forest-savannah mosaic) and Gyankobaa (forest), with S. squamosum or S. sanctipauli being the predominant species, respectively. In Bosomase (southern forest region) only S. sanctipauli was collected in the 2009 wet season, but in the 2010 dry season S. yahense was also caught. MBRs ranged from 714 bites/person/month at Agborlekame (100% S. damnosum s.s./S. sirbanum) to 8,586 bites/person/month at Pillar 83/Djodji (98.5% S. squamosum). MBRs were higher in the wet season. In contrast, parous rates were higher in the dry season (41.8% vs. 18.4%), resulting in higher MPBRs in the dry season. Daily host-seeking activity of S. damnosum s.s./S. sirbanum was bimodal, whilst S. squamosum and S. sanctipauli had unimodal afternoon peaks. Conclusions: The bionomic differences between sibling species of the S. damnosum complex need to be taken into account when designing entomological monitoring protocols for interventions and parameterising mathematical models for onchocerciasis control and elimination

Combining motion analysis and microfluidics--a novel approach for detecting whole-animal responses to test substances.

Small, early life stages, such as zebrafish embryos are increasingly used to assess the biological effects of chemical compounds in vivo. However, behavioural screens of such organisms are challenging in terms of both data collection (culture techniques, drug delivery and imaging) and data evaluation (very large data sets), restricting the use of high throughput systems compared to in vitro assays. Here, we combine the use of a microfluidic flow-through culture system, or BioWell plate, with a novel motion analysis technique, (sparse optic flow - SOF) followed by spectral analysis (discrete Fourier transformation - DFT), as a first step towards automating data extraction and analysis for such screenings. Replicate zebrafish embryos housed in a BioWell plate within a custom-built imaging system were subject to a chemical exposure (1.5% ethanol). Embryo movement was videoed before (30 min), during (60 min) and after (60 min) exposure and SOF was then used to extract data on movement (angles of rotation and angular changes to the centre of mass of embryos). DFT was subsequently used to quantify the movement patterns exhibited during these periods and Multidimensional Scaling and ANOSIM were used to test for differences. Motion analysis revealed that zebrafish had significantly altered movements during both the second half of the alcohol exposure period and also the second half of the recovery period compared to their pre-treatment movements. Manual quantification of tail flicking revealed the same differences between exposure-periods as detected using the automated approach. However, the automated approach also incorporates other movements visible in the organism such as blood flow and heart beat, and has greater power to discern environmentally-driven changes in the behaviour and physiology of organisms. We suggest that combining these technologies could provide a highly efficient, high throughput assay, for assessing whole embryo responses to various drugs and chemicals

Both the Caspase CSP-1 and a Caspase-Independent Pathway Promote Programmed Cell Death in Parallel to the Canonical Pathway for Apoptosis in Caenorhabditis elegans

Caspases are cysteine proteases that can drive apoptosis in metazoans and have critical functions in the elimination of cells during development, the maintenance of tissue homeostasis, and responses to cellular damage. Although a growing body of research suggests that programmed cell death can occur in the absence of caspases, mammalian studies of caspase-independent apoptosis are confounded by the existence of at least seven caspase homologs that can function redundantly to promote cell death. Caspase-independent programmed cell death is also thought to occur in the invertebrate nematode Caenorhabditis elegans. The C. elegans genome contains four caspase genes (ced-3, csp-1, csp-2, and csp-3), of which only ced-3 has been demonstrated to promote apoptosis. Here, we show that CSP-1 is a pro-apoptotic caspase that promotes programmed cell death in a subset of cells fated to die during C. elegans embryogenesis. csp-1 is expressed robustly in late pachytene nuclei of the germline and is required maternally for its role in embryonic programmed cell deaths. Unlike CED-3, CSP-1 is not regulated by the APAF-1 homolog CED-4 or the BCL-2 homolog CED-9, revealing that csp-1 functions independently of the canonical genetic pathway for apoptosis. Previously we demonstrated that embryos lacking all four caspases can eliminate cells through an extrusion mechanism and that these cells are apoptotic. Extruded cells differ from cells that normally undergo programmed cell death not only by being extruded but also by not being engulfed by neighboring cells. In this study, we identify in csp-3; csp-1; csp-2 ced-3 quadruple mutants apoptotic cell corpses that fully resemble wild-type cell corpses: these caspase-deficient cell corpses are morphologically apoptotic, are not extruded, and are internalized by engulfing cells. We conclude that both caspase-dependent and caspase-independent pathways promote apoptotic programmed cell death and the phagocytosis of cell corpses in parallel to the canonical apoptosis pathway involving CED-3 activation.Howard Hughes Medical InstituteDamon Runyon Cancer Research FoundationCharles A. King Trus

Regional conditions cause contrasting behaviour in U-isotope fractionation in black shales: Constraints for global ocean palaeo-redox reconstructions

The U-isotope system is a well-established palaeo-redox proxy that potentially constrains the global extent of marine anoxia during average as well as extreme redox events throughout Earth's history. A typical archive that forms underneath a reducing water column and acts as an intense U sink is organic-rich black shale. However, the degree to which black shale archives reflect the marine U-isotope signature is not well understood because U-isotope fractionation between U(VI)-bearing seawater and U(IV)-bearing black shales may vary as a function of local environmental conditions. Here, we present a combination of U-isotope and elemental concentration datasets, supported by a complementary Mo-isotope record, for the Furlo sedimentary section in Marche–Umbria, Italy and interrogate the combined systematics to unravel the mechanisms controlling the U-isotope fractionation factor between black shales and ambient seawater. We examine black shales deposited before and during Oceanic Anoxic Event 2 (OAE 2), which was one of the most extreme climatic perturbations of the Mesozoic Era that took place around the Cenomanian–Turonian boundary (Late Cretaceous, c. 94 Ma). The results of this study show that the U-isotope signature in the black shales deposited before OAE 2 was controlled by different mechanisms than the U-isotope ratios recorded in black shales deposited during OAE 2, with both stratigraphic intervals likely influenced by local environmental conditions. Probable local environmental changes include increased U reduction associated with biomass at or above the sediment–water interface and varying dissolved hydrogen sulphide concentrations in the water column and sediment. The overall results of this study confirm that black shales are a highly complex archive for U-isotope studies of past oceanic redox conditions, due to the sensitivity of the U-isotope fractionation mechanism to local environmental conditions, which are difficult to constrain. We propose the application of a ∆238Ushale-seawater of 0.6 ± 0.1 ‰ to black shale records deposited under locally constant euxinic conditions at non-restricted settings

Epithelial damage and tissue γδ T cells promote a unique tumor-protective IgE response

IgE is an ancient and conserved immunoglobulin isotype with potent immunological function. Nevertheless, the regulation of IgE responses remains an enigma, and evidence of a role for IgE in host defense is limited. Here we report that topical exposure to a common environmental DNA-damaging xenobiotic initiated stress surveillance by γδTCR+ intraepithelial lymphocytes that resulted in class switching to IgE in B cells and the accumulation of autoreactive IgE. High-throughput antibody sequencing revealed that γδ T cells shaped the IgE repertoire by supporting specific variable-diversity-joining (VDJ) rearrangements with unique characteristics of the complementarity-determining region CDRH3. This endogenous IgE response, via the IgE receptor FcεRI, provided protection against epithelial carcinogenesis, and expression of the gene encoding FcεRI in human squamous-cell carcinoma correlated with good disease prognosis. These data indicate a joint role for immunosurveillance by T cells and by B cells in epithelial tissues and suggest that IgE is part of the host defense against epithelial damage and tumor development