Experiments in terabyte searching, genomic retrieval and novelty detection for TREC 2004

In TREC2004, Dublin City University took part in three tracks, Terabyte (in collaboration with University College Dublin), Genomic and Novelty. In this paper we will discuss each track separately and present separate conclusions from this work. In addition, we present a general description of a text retrieval engine that we have developed in the last year to support our experiments into large scale, distributed information retrieval, which underlies all of the track experiments described in this document

TRECVID 2004 experiments in Dublin City University

In this paper, we describe our experiments for TRECVID 2004 for the Search task. In the interactive search task, we developed two versions of a video search/browse system based on the Físchlár Digital Video System: one with text- and image-based searching (System A); the other with only image (System B). These two systems produced eight interactive runs. In addition we submitted ten fully automatic supplemental runs and two manual runs. A.1, Submitted Runs: • DCUTREC13a_{1,3,5,7} for System A, four interactive runs based on text and image evidence. • DCUTREC13b_{2,4,6,8} for System B, also four interactive runs based on image evidence alone. • DCUTV2004_9, a manual run based on filtering faces from an underlying text search engine for certain queries. • DCUTV2004_10, a manual run based on manually generated queries processed automatically. • DCU_AUTOLM{1,2,3,4,5,6,7}, seven fully automatic runs based on language models operating over ASR text transcripts and visual features. • DCUauto_{01,02,03}, three fully automatic runs based on exploring the benefits of multiple sources of text evidence and automatic query expansion. A.2, In the interactive experiment it was confirmed that text and image based retrieval outperforms an image-only system. In the fully automatic runs, DCUauto_{01,02,03}, it was found that integrating ASR, CC and OCR text into the text ranking outperforms using ASR text alone. Furthermore, applying automatic query expansion to the initial results of ASR, CC, OCR text further increases performance (MAP), though not at high rank positions. For the language model-based fully automatic runs, DCU_AUTOLM{1,2,3,4,5,6,7}, we found that interpolated language models perform marginally better than other tested language models and that combining image and textual (ASR) evidence was found to marginally increase performance (MAP) over textual models alone. For our two manual runs we found that employing a face filter disimproved MAP when compared to employing textual evidence alone and that manually generated textual queries improved MAP over fully automatic runs, though the improvement was marginal. A.3, Our conclusions from our fully automatic text based runs suggest that integrating ASR, CC and OCR text into the retrieval mechanism boost retrieval performance over ASR alone. In addition, a text-only Language Modelling approach such as DCU_AUTOLM1 will outperform our best conventional text search system. From our interactive runs we conclude that textual evidence is an important lever for locating relevant content quickly, but that image evidence, if used by experienced users can aid retrieval performance. A.4, We learned that incorporating multiple text sources improves over ASR alone and that an LM approach which integrates shot text, neighbouring shots and entire video contents provides even better retrieval performance. These findings will influence how we integrate textual evidence into future Video IR systems. It was also found that a system based on image evidence alone can perform reasonably and given good query images can aid retrieval performance

Three dimensional tracking for volumetric spectral-domain optical coherence tomography

We present a three-dimensional (3D) tracker for a clinical ophthalmic spectral domain optical coherence tomography (SD-OCT) system that combines depth-tracking with lateral tracking, providing a stabilized reference frame for 3D data recording and post acquisition analysis. The depth-tracking system is implemented through a real-time dynamic feedback mechanism to compensate for motion artifact in the axial direction. Active monitoring of the retina and adapting the reference arm of the interferometer allowed the whole thickness of the retina to be stabilized to within +/- 100 mu m. We achieve a relatively constant SNR from image to image by stabilizing the image of the retina with respect to the depth dependent sensitivity of SD-OCT. The depth tracking range of our system is 5.2 mm in air and the depth is adjusted every frame. Enhancement in the stability of the images with the depth-tracking algorithm is demonstrated on a healthy volunteer.X1119sciescopu

A mechanism for morphogen-controlled domain growth

Many developmental systems are organised via the action of graded distributions of morphogens. In the Drosophila wing disc, for example, recent experimental evidence has shown that graded expression of the morphogen Dpp controls cell proliferation and hence disc growth. Our goal is to explore a simple model for regulation of wing growth via the Dpp gradient: we use a system of reaction-diffusion equations to model the dynamics of Dpp and its receptor Tkv, with advection arising as a result of the flow generated by cell proliferation. We analyse the model both numerically and analytically, showing that uniform domain growth across the disc produces an exponentially growing wing disc

Impact of Salmonid alphavirus infection in diploid and triploid Atlantic salmon (Salmo salar L.) fry

With increasing interest in the use of triploid salmon in commercial aquaculture, gaining an understanding of how economically important pathogens affect triploid stocks is important. To compare the susceptibility of diploid and triploid Atlantic salmon (Salmo salar L.) to viral pathogens, fry were experimentally infected with Salmonid alphavirus sub-type 1 (SAV1), the aetiological agent of pancreas disease (PD) affecting Atlantic salmon aquaculture in Europe. Three groups of fry were exposed to the virus via different routes of infection: intraperitoneal injection (IP), bath immersion, or cohabitation (co-hab) and untreated fry were used as a control group. Mortalities commenced in the co-hab challenged diploid and triploid fish from 11 days post infection (dpi), and the experiment was terminated at 17 dpi. Both diploid and triploid IP challenged groups had similar levels of cumulative mortality at the end of the experimental period (41.1 % and 38.9 % respectively), and these were significantly higher (p < 0.01) than for the other challenge routes. A TaqMan-based quantitative PCR was used to assess SAV load in the heart, a main target organ of the virus, and also liver, which does not normally display any pathological changes during clinical infections, but exhibited severe degenerative lesions in the present study. The median viral RNA copy number was higher in diploid fish compared to triploid fish in both the heart and the liver of all three challenged groups. However, a significant statistical difference (p < 0.05) was only apparent in the liver of the co-hab groups. Diploid fry also displayed significantly higher levels of pancreatic and myocardial degeneration than triploids. This study showed that both diploid and triploid fry are susceptible to experimental SAV1 infection. The lower virus load seen in the triploids compared to the diploids may possibly be related to differences in cell metabolism between the two groups, however, further investigation is necessary to confirm this and also to assess the outcome of PD outbreaks in other developmental stages of the fish when maintained in commercial production systems

Habitable Zones of Host Stars During the Post-MS Phase

A star will become brighter and brighter with stellar evolution, and the distance of its habitable zone will become farther and farther. Some planets outside the habitable zone of a host star during the main sequence phase may enter the habitable zone of the host star during other evolutionary phases. A terrestrial planet within the habitable zone of its host star is generally thought to be suited to life existence. Furthermore, a rocky moon around a giant planet may be also suited to life survive, provided that the planet-moon system is within the habitable zone of its host star. Using Eggleton's code and the boundary flux of habitable zone, we calculate the habitable zone of our Solar after the main sequence phase. It is found that Mars' orbit and Jupiter's orbit will enter the habitable zone of Solar during the subgiant branch phase and the red giant branch phase, respectively. And the orbit of Saturn will enter the habitable zone of Solar during the He-burning phase for about 137 million years. Life is unlikely at any time on Saturn, as it is a giant gaseous planet. However, Titan, the rocky moon of Saturn, may be suitable for biological evolution and become another Earth during that time. For low-mass stars, there are similar habitable zones during the He-burning phase as our Solar, because there are similar core masses and luminosities for these stars during that phase.Comment: 6 pages, 7 figures. Accepted by Ap & S

The compound Poisson limit ruling periodic extreme behaviour of non-uniformly hyperbolic dynamics

We prove that the distributional limit of the normalised number of returns to small neighbourhoods of periodic points of non-uniformly hyperbolic dynamical systems is compound Poisson. The returns to small balls around a fixed point in the phase space correspond to the occurrence of rare events, or exceedances of high thresholds, so that there is a connection between the laws of Return Times Statistics and Extreme Value Laws. The fact that the fixed point in the phase space is a repelling periodic point implies that there is a tendency for the exceedances to appear in clusters whose average sizes is given by the Extremal Index, which depends on the expansion of the system at the periodic point. We recall that for generic points, the exceedances, in the limit, are singular and occur at Poisson times. However, around periodic points, the picture is different: the respective point processes of exceedances converge to a compound Poisson process, so instead of single exceedances, we have entire clusters of exceedances occurring at Poisson times with a geometric distribution ruling its multiplicity. The systems to which our results apply include: general piecewise expanding maps of the interval (Rychlik maps), maps with indifferent fixed points (Manneville-Pomeau maps) and Benedicks-Carleson quadratic maps.Comment: To appear in Communications in Mathematical Physic

Habitable Zones and UV Habitable Zones around Host Stars

Ultraviolet radiation is a double-edged sword to life. If it is too strong, the terrestrial biological systems will be damaged. And if it is too weak, the synthesis of many biochemical compounds can not go along. We try to obtain the continuous ultraviolet habitable zones, and compare the ultraviolet habitable zones with the habitable zones of host stars. Using the boundary ultraviolet radiation of ultraviolet habitable zone, we calculate the ultraviolet habitable zones of host stars with masses from 0.08 to 4.00 \mo. For the host stars with effective temperatures lower than 4,600 K, the ultraviolet habitable zones are closer than the habitable zones. For the host stars with effective temperatures higher than 7,137 K, the ultraviolet habitable zones are farther than the habitable zones. For hot subdwarf as a host star, the distance of the ultraviolet habitable zone is about ten times more than that of the habitable zone, which is not suitable for life existence.Comment: 5 pages, 3 figure

Seasonal development and pathological changes associated with the parasitic nematode Philometroides sanguineus in wild crucian carp Carassius carassius (L.) in England

Pathological changes associated with the parasitic nematode Philometroides sanguineus (Rudolphi, 1819) are described for the first time from observations of infections in wild crucian carp Carassius carassius (L.) in England. The damage caused by P. sanguineus was influenced strongly by host size, parasite development and the seasonal migrations of female nematodes within host tissues. Male and unfertilized female nematodes located on the swim-bladder wall caused only minor, localized changes. In contrast, the migration of gravid female nematodes into the fins during autumn provoked an acute inflammatory response comprising neutrophils, eosinophils and lymphocytes. This was accompanied by fin distortion, swelling of the dorsal and caudal tissues, degenerative changes and localized oedema. The encapsulation of female nematodes in connective tissue throughout winter limited additional tissue damage. The emergence of gravid nematodes from the fins in spring to facilitate larval dispersal caused necrosis, hyperplasia and loss of skin integrity. This activity was again accompanied by acute inflammatory reactions. Pathological changes were more severe in crucian carp measuring less than 60 mm in length, with no signs of debilitation in larger fish. These observations suggest that any impact of P. sanguineus is strictly seasonal and may be limited to fry. Lesions caused by this parasite, only recently recorded in Britain, may represent an additional pressure upon wild crucian carp populations already threatened by hybridization, competition and habitat loss

Nutrigenomics, the microbiome, and gene-environment interactions: New directions in cardiovascular disease research, prevention, and treatment

Cardiometabolic diseases are the leading cause of death worldwide and are strongly linked to both genetic and nutritional factors. The field of nutrigenomics encompasses multiple approaches aimed at understanding the effects of diet on health or disease development, including nutrigenetic studies investigating the relationship between genetic variants and diet in modulating cardiometabolic risk, as well as the effects of dietary components on multiple "omic" measures, including transcriptomics, metabolomics, proteomics, lipidomics, epigenetic modifications, and the microbiome. Here, we describe the current state of the field of nutrigenomics with respect to cardiometabolic disease research and outline a direction for the integration of multiple omics techniques in future nutrigenomic studies aimed at understanding mechanisms and developing new therapeutic options for cardiometabolic disease treatment and prevention