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

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,

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

Asymptotic Equivalence of Nonparametric Regression and White Noise

The principal result is that, under conditions, to any nonparametric regression problem there corresponds an asymptotically equivalent sequence of white noise with drift problems, and conversely. This asymptotic equivalence is in a global and uniform sense. Any normalized risk function attainable in one problem is asymptotically attainable in the other, with the difference in normalized risks converging to zero uniformly over the entire parameter space. The results are constructive. A recipe is provided for producing these asymptotically equivalent procedures. Some implications and generalizations of the principal result are also discussed

Information Inequality Bounds on the Minimax Risk (With an Application to Nonparametric Regression)

This paper compares three methods for producing lower bounds on the minimax risk under quadratic loss. The first uses the bounds from Brown and Gajek. The second method also uses the information inequality and results in bounds which are always at least as good as those from the first method. The third method is the hardest-linear-family method described by Donoho and Liu. These methods are applied in four examples, the last of which relates to a frequently considered problem in nonparametric regression

Leaf Detritus Processing in an Ozark Cave Stream

Detritus processing rates and mechanisms were investigated in an Ozark cave stream using post oak (Quercus stellata) leaf packs. The 5 g leaf packs lost ca. 30% of their dry weight within 84 days, resulting in a calculated K value of 0.05. This was an unexpectedly high rate of utilization. Diversity of invertebrates associated with the leaf packs was very low. Stygobromus ozarkensis (Amphipoda) was the only shredder. The two isopods, Caecidotea stiladactyla and Lirceus sp. were the only collectors observed other than a single species of oligochaete worm. Our data indicated that leaf detritus processing rates are virtually independent of the number of types of invertebrates associated with the leaf packs

A Constrained Risk Inequality With Applications to Nonparametric Functional Estimation

A general constrained minimum risk inequality is derived. Given two densities fθ and f0 we find a lower bound for the risk at the point θ given an upper bound for the risk at the point 0. The inequality sheds new light on superefficient estimators in the normal location problem and also on an adaptive estimation problem arising in nonparametric functional estimation

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