Towards a lightweight generic computational grid framework for biological research

Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project

Equivalence theory for density estimation, Poisson processes and Gaussian white noise with drift

This paper establishes the global asymptotic equivalence between a Poisson process with variable intensity and white noise with drift under sharp smoothness conditions on the unknown function. This equivalence is also extended to density estimation models by Poissonization. The asymptotic equivalences are established by constructing explicit equivalence mappings. The impact of such asymptotic equivalence results is that an investigation in one of these nonparametric models automatically yields asymptotically analogous results in the other models.Comment: Published at http://dx.doi.org/10.1214/009053604000000012 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Local drinking water filters reduce diarrheal disease in Cambodia: a randomized, controlled trial of the ceramic water purifier.

A randomized, controlled intervention trial of two household-scale drinking water filters was conducted in a rural village in Cambodia. After collecting four weeks of baseline data on household water quality, diarrheal disease, and other data related to water use and handling practices, households were randomly assigned to one of three groups of 60 households: those receiving a ceramic water purifier (CWP), those receiving a second filter employing an iron-rich ceramic (CWP-Fe), and a control group receiving no intervention. Households were followed for 18 weeks post-baseline with biweekly follow-up. Households using either filter reported significantly less diarrheal disease during the study compared with a control group of households without filters as indicated by longitudinal prevalence ratios CWP: 0.51 (95% confidence interval [CI]: 0.41-0.63); CWP-Fe: 0.58 (95% CI: 0.47-0.71), an effect that was observed in all age groups and both sexes after controlling for clustering within households and within individuals over time

Pediatric Cardiac Tumors: A 45-year, Single Institution Review

Background: Cardiac tumors in children are rare. Of the cases reported in the literature, nearly all are benign and managed conservatively. Methods: This is a retrospective, observational study of pediatric patients <18 years who presented for surgical evaluation of a cardiac tumor, between 1969 and 2014 at a tertiary care children’s hospital. Presentation, pathology, management, and outcomes were evaluated. Results: Over the last 45 years, 64 patients were evaluated for surgical resection of a cardiac tumor. Rhabdomyoma was the most common neoplasm (58%), and 17% of the tumors had malignant pathologies. While 42% of benign cardiac neoplasms required surgical intervention for significant hemodynamic concerns, 73% of malignant neoplasms underwent radical excision, if possible, followed by adjuvant chemotherapy. Despite a 37% mortality in patients with malignant pathology, an aggressive surgical approach can yield long-term survival in some patients. There were no deaths among patients with benign tumors and 17% had postoperative complications mostly related to mitral regurgitation. Conclusion: Cardiac tumors in children are rare but can be managed aggressively with good outcomes. Benign tumors have an excellent survival with most complications related to tumor location. Malignant tumors have a high mortality rate, but surgery and adjuvant chemotherapy allow for prolonged survival in selected patients

Challenges and solutions for Latin named entity recognition

Although spanning thousands of years and genres as diverse as liturgy, historiography, lyric and other forms of prose and poetry, the body of Latin texts is still relatively sparse compared to English. Data sparsity in Latin presents a number of challenges for traditional Named Entity Recognition techniques. Solving such challenges and enabling reliable Named Entity Recognition in Latin texts can facilitate many down-stream applications, from machine translation to digital historiography, enabling Classicists, historians, and archaeologists for instance, to track the relationships of historical persons, places, and groups on a large scale. This paper presents the first annotated corpus for evaluating Named Entity Recognition in Latin, as well as a fully supervised model that achieves over 90% F-score on a held-out test set, significantly outperforming a competitive baseline. We also present a novel active learning strategy that predicts how many and which sentences need to be annotated for named entities in order to attain a specified degree of accuracy when recognizing named entities automatically in a given text. This maximizes the productivity of annotators while simultaneously controlling quality

The relationship between import and retail prices: a case study of fresh grapefruit in Japan

The study examined the relationship between import price and retail price of grapefruit in Japan. Estimated retail-import price relationship indicate asymmetry responses distributed over time. Import price changes are not fully transmitted to the retail level, with import price increases being passed on more fully than import price decreases.fresh grapefruit, Japan, import and retail price transmission, Demand and Price Analysis, International Relations/Trade,

Receptive Field Block Net for Accurate and Fast Object Detection

Current top-performing object detectors depend on deep CNN backbones, such as ResNet-101 and Inception, benefiting from their powerful feature representations but suffering from high computational costs. Conversely, some lightweight model based detectors fulfil real time processing, while their accuracies are often criticized. In this paper, we explore an alternative to build a fast and accurate detector by strengthening lightweight features using a hand-crafted mechanism. Inspired by the structure of Receptive Fields (RFs) in human visual systems, we propose a novel RF Block (RFB) module, which takes the relationship between the size and eccentricity of RFs into account, to enhance the feature discriminability and robustness. We further assemble RFB to the top of SSD, constructing the RFB Net detector. To evaluate its effectiveness, experiments are conducted on two major benchmarks and the results show that RFB Net is able to reach the performance of advanced very deep detectors while keeping the real-time speed. Code is available at https://github.com/ruinmessi/RFBNet.Comment: Accepted by ECCV 201

Positron detection in silica monoliths for miniaturised quality control of PET radiotracers

We demonstrate the use of the miniaturised Medipix positron sensor for detection of the clinical PET radiotracer, [⁶⁸Ga]gallium-citrate, on a silica-based monolith, towards microfluidic quality control. The system achieved a far superior signal-to-noise ratio compared to conventional sodium iodide-based radio-HPLC detection and allowed real-time visualisation of positrons in the monolith

Spectrophotometric analysis of ternary uranyl systems to replace tri-N-butyl phosphate (TBP) in used fuel reprocessing

In this report, the interaction of monoamide/diamide and monoamide/diglycolamide mixtures with UO2+2 are investigated in pH = 1 methanolic nitric acid media. These monoamides include N,N-dimethylacetamide (DMAA), N,N-diethylacetamide (DEAA), N,N-dibutylacetamide (DBAA) and N,N-dibutylbutanamide (DBBA). N,N,N′N′-tetraethylmalonamide (TEMA) and N,N,N′,N′-tetraethyldiglycolamide (TEDGA), which were chosen as model diamides and diglycolamides, respectively. Complex stability constants for each ligand were modelled using the Stability Quotients Using Absorbance Data program using UV–visible data. Complex stoichiometry of ligand mixtures was determined using Job plots and UV–Vis spectrometry. Monoamides were confirmed to produce only disolvate complexes with UO2+2 in solution. The log10(K) values for monoamides were found to be independent of amine-side chain length, but were slightly dependent on the carbonyl-side chain length. TEDGA was found to produce multiple uranyl complexes in solution. Job plot data indicated that the uranyl cation strongly prefers to bond either only with the monoamide or diamide in ternary monoamide–diamide–UO2 systems. Monoamide–diglycolamide–UO2 systems were more complicated, with Job plot data indicating the potential for multiple ternary species being present is dependent on the monoamide structure

Heterolytic H_2 Activation Mediated by Low-Coordinate L_3Fe-(µ-N)-FeL_3 Complexes to Generate Fe(µ-NH)(µ-H)Fe Species

The diiron μ-nitride complexes, {L_3Fe^(II)(μ-N)Fe^(II)L_3}- and L_3Fe^(III)(μ-N)Fe^(II)L_3, heterolytically activate hydrogen (1 atm) at ambient temperature in solution (L_3 = [PhB(CH_2PPh_2)_3]-). These transformations lead to structurally unique {L_3Fe^(II)(μ-NH)(μ-H)Fe^(II)L^3}- and L_3Fe^(III)(μ-NH)(μ-H)Fe^(II)L_3 products. X-ray data establish a marked reduction in the Fe−Fe distance upon H_2 uptake, and spectroscopic data establish both Fe^(II)Fe^(II) species to be diamagnetic, whereas the Fe^(III)Fe^(II) species, L_3Fe^(III)(μ-N)Fe^(II)L_3 and L_3Fe^(III)(μ-NH)(μ-H)Fe^(II)L_3, populate doublet ground states with thermally accessible higher spin states