Visualising the structure of document search results: A comparison of graph theoretic approaches

This is the post-print of the article - Copyright @ 2010 Sage PublicationsPrevious work has shown that distance-similarity visualisation or ‘spatialisation’ can provide a potentially useful context in which to browse the results of a query search, enabling the user to adopt a simple local foraging or ‘cluster growing’ strategy to navigate through the retrieved document set. However, faithfully mapping feature-space models to visual space can be problematic owing to their inherent high dimensionality and non-linearity. Conventional linear approaches to dimension reduction tend to fail at this kind of task, sacrificing local structural in order to preserve a globally optimal mapping. In this paper the clustering performance of a recently proposed algorithm called isometric feature mapping (Isomap), which deals with non-linearity by transforming dissimilarities into geodesic distances, is compared to that of non-metric multidimensional scaling (MDS). Various graph pruning methods, for geodesic distance estimation, are also compared. Results show that Isomap is significantly better at preserving local structural detail than MDS, suggesting it is better suited to cluster growing and other semantic navigation tasks. Moreover, it is shown that applying a minimum-cost graph pruning criterion can provide a parameter-free alternative to the traditional K-neighbour method, resulting in spatial clustering that is equivalent to or better than that achieved using an optimal-K criterion

A phase II study of capecitabine and oxalplatin combination chemotherapy in patients with inoperable adenocarcinoma of the gall bladder or biliary tract

Background: Advanced biliary tract carcinomas are associated with a poor prognosis, and palliative chemotherapy has only modest benefit. This multi-centre phase II study was conducted to determine the efficacy of capecitabine in combination with oxaliplatin in patients with inoperable gall bladder or biliary tract cancer. Methods: This was a Phase II, non-randomised, two-stage Simon design, multi-centre study. Ethics approval was sought and obtained by the North West MREC, and then locally by the West Glasgow Hospitals Research Ethics Com mittee. Eligible patients with inoperable locally advanced or metastatic adenocarcinoma of the gall bladder or biliary tract and with adequate performance status, haematologic, renal, and hepatic function were treated with capecit abine (1000 mg/m2 po, twice daily, days 1–14) and oxaliplatin (130 mg/m2 i.v., day 1) every 3 weeks for up to six cycles. The primary objective of the study was to determine the objective tumour response rates (complete and partial). The secondary objectives included assessment of toxicity, progression-free survival, and overall survival. Results: Forty-three patients were recruited between July 2003 and December 2005. The regimen was well tolerated with no grade 3/4 neutropenia or thrombocytopenia. Grade 3/4 sensory neuropathy was observed in six patients. Two-thirds of patients received their chemotherapy without any dose delays. Overall response rate was 23.8 % (95 % CI 12.05–39.5 %). Stable disease was observed in a further 13 patients (31 %) and progressive disease observed in 12 (28.6 %) of patients. The median progression-free survival was 4.6 months (95 % CI 2.8–6.4 months; Fig. 1) and the median overall survival 7.9 months (95 % CI 5.3–10.4 months; Fig. 2). Conclusion: Capecitabine combined with oxaliplatin has a lower disease control and shorter overall survival than the combination of cisplatin with gemcitabine which has subsequently become the standard of care in this disease. How ever, capecitabine in combination with oxaliplatin does have modest activity in this disease, and can be considered as an alternative treatment option for patients in whom cisplatin and/or gemcitabine are contra-indicated

Rotational Feshbach Resonances in Ultracold Molecular Collisions

In collisions at ultralow temperatures, molecules will possess Feshbach resonances, foreign to ultracold atoms, whose virtual excited states consist of rotations of the molecules. We estimate the mean spacing and mean widths of these resonant states, exploiting the fact the molecular collisions at low energy display chaotic motion. As examples, we consider the experimentally relevant molecules O_2, OH, and PbO. The density of s-wave resonant states for these species is quite high, implying that a large number of narrow resonant states will exist.Comment: 4 pages, 2 figure

Peptide-Tetrapyrrole Supramolecular Self-Assemblies: State of the Art.

The covalent and noncovalent association of self-assembling peptides and tetrapyrroles was explored as a way to generate systems that mimic Nature's functional supramolecular structures. Different types of peptides spontaneously assemble with porphyrins, phthalocyanines, or corroles to give long-range ordered architectures, whose structure is determined by the features of both components. The regular morphology and ordered molecular arrangement of these systems enhance the photochemical properties of embedded chromophores, allowing applications as photo-catalysts, antennas for dye-sensitized solar cells, biosensors, and agents for light-triggered therapies. Chemical modifications of peptide and tetrapyrrole structures and control over the assembly process can steer the organization and influence the properties of the resulting system. Here we provide a review of the field, focusing on the assemblies obtained from different classes of self-assembling peptides with tetrapyrroles, their morphologies and their applications as innovative functional materials

National-scale detection of reservoir impacts through hydrological signatures

Reservoirs play a vital role in the supply and management of water resources and their operation can significantly alter downstream flow. Despite this, reservoirs are frequently excluded or poorly represented in large-scale hydrological models, which can be partly attributed to a lack of open-access data describing reservoir operations, inflow and storage. To help inform the development of reservoir operation schemes, we collate a suite of hydrological signatures designed to detect the impacts of reservoirs on the flow regime at large-scales from downstream flow records only. By removing the need for pre-and-post-reservoir flow timeseries (a requirement of many pre-existing techniques), these signatures facilitate the assessment of flow alteration across a much wider range of catchments. To demonstrate their application, we calculate the signatures across Great Britain in 111 benchmark (i.e., near-natural) catchments and 186 reservoir catchments (where at least one upstream reservoir is present). We find that abstractions from water resource reservoirs induce deficits in the water balance, and that pre-defined flow releases (e.g., the compensation flow) reduce variability in the downstream flow duration curve and in intra-annual low flows. By comparing signatures in benchmark and reservoir catchments, we define thresholds above which the influence of reservoirs can be distinguished from natural variability and identify 40 catchments significantly impacted by the presence of reservoirs. The signatures also provide insights into local reservoir operations, which can inform the development of tailored reservoir operation schemes, and identify locations where current modeling practices (which lack reservoir representation) will be insufficient

Fluorescent Risedronate Analogues Reveal Bisphosphonate Uptake by Bone Marrow Monocytes and Localization Around Osteocytes In Vivo

Bisphosphonates are effective antiresorptive agents owing to their bone-targeting property and ability to inhibit osteoclasts. It remains unclear, however, whether any non-osteoclast cells are directly affected by these drugs in vivo. Two fluorescent risedronate analogues, carboxyfluorescein-labeled risedronate (FAM-RIS) and Alexa Fluor 647–labeled risedronate (AF647-RIS), were used to address this question. Twenty-four hours after injection into 3-month-old mice, fluorescent risedronate analogues were bound to bone surfaces. More detailed analysis revealed labeling of vascular channel walls within cortical bone. Furthermore, fluorescent risedronate analogues were present in osteocytic lacunae in close proximity to vascular channels and localized to the lacunae of newly embedded osteocytes close to the bone surface. Following injection into newborn rabbits, intracellular uptake of fluorescently labeled risedronate was detected in osteoclasts, and the active analogue FAM-RIS caused accumulation of unprenylated Rap1A in these cells. In addition, CD14high bone marrow monocytes showed relatively high levels of uptake of fluorescently labeled risedronate, which correlated with selective accumulation of unprenylated Rap1A in CD14+ cells, as well as osteoclasts, following treatment with risedronate in vivo. Similar results were obtained when either rabbit or human bone marrow cells were treated with fluorescent risedronate analogues in vitro. These findings suggest that the capacity of different cell types to endocytose bisphosphonate is a major determinant for the degree of cellular drug uptake in vitro as well as in vivo. In conclusion, this study shows that in addition to bone-resorbing osteoclasts, bisphosphonates may exert direct effects on bone marrow monocytes in vivo. © 2010 American Society for Bone and Mineral Researc

Keck-Nirspec Infrared OH Lines: Oxygen Abundances in Metal-Poor Stars Down to [Fe/H] = -2.9

Infrared OH lines at 1.5 - 1.7 um in the H band were obtained with the NIRSPEC high-resolution spectrograph at the 10m Keck Telescope for a sample of seven metal-poor stars. Detailed analyses have been carried out, based on optical high-resolution data obtained with the FEROS spectrograph at ESO. Stellar parameters were derived by adopting infrared flux method effective temperatures, trigonometric and/or evolutionary gravities and metallicities from FeII lines. We obtain that the sample stars with metallicities [Fe/H] < -2.2 show a mean oxygen abundance [O/Fe] ~ 0.54, for a solar oxygen abundance of epsilon(O) = 8.87, or [O/Fe] ~ 0.64 if epsilon(O) = 8.77 is assumed.Comment: To be published in ApJ 575 (August 10

Associations between vision impairment and driving and the effectiveness of vision-related interventions : protocol for a systematic review and meta-analysis

Introduction Driving is one of the main modes of transport with safe driving requiring a combination of visual, cognitive and physical skills. With population ageing, the number of people living with vision impairment is set to increase in the decades ahead. Vision impairment may negatively impact an individual's ability to safely drive. The association between vision impairment and motor vehicle crash involvement or driving participation has yet to be systematically investigated. Further, the evidence for the effectiveness of vision-related interventions aimed at decreasing crashes and driving errors has not been synthesised. Methods and analysis A search will be conducted for relevant studies on Medline (Ovid), EMBASE and Global Health from their inception to March 2020 without date or geographical restrictions. Two investigators will independently screen abstracts and full texts using Covidence software with conflicts resolved by a third investigator. Data extraction will be conducted on all included studies, and their quality assessed to determine the risk of bias using the Joanna Briggs Institute Critical Appraisal Tools. Outcome measures include crash risk, driving cessation and surrogate measures of driving safety (eg, driving errors and performance). The results of this review will be reported using the Preferred Reporting Items for Systematic Review and Meta-Analysis guideline. Meta-analysis will be undertaken for outcomes with sufficient data and reported following the Meta-analyses of Observational Studies in Epidemiology guideline. Where statistical pooling is not feasible or appropriate, narrative summaries will be presented following the Synthesis Without Meta-analysis in systematic reviews guideline. Ethics and dissemination This review will only report on published data thus no ethics approval is required. Results will be included in the Lancet Global Health Commission on Global Eye Health, published in a peer-reviewed journal and presented at relevant conferences. PROSPERO registration number CRD42020172153