Machine Learning in Automated Text Categorization

The automated categorization (or classification) of texts into predefined categories has witnessed a booming interest in the last ten years, due to the increased availability of documents in digital form and the ensuing need to organize them. In the research community the dominant approach to this problem is based on machine learning techniques: a general inductive process automatically builds a classifier by learning, from a set of preclassified documents, the characteristics of the categories. The advantages of this approach over the knowledge engineering approach (consisting in the manual definition of a classifier by domain experts) are a very good effectiveness, considerable savings in terms of expert manpower, and straightforward portability to different domains. This survey discusses the main approaches to text categorization that fall within the machine learning paradigm. We will discuss in detail issues pertaining to three different problems, namely document representation, classifier construction, and classifier evaluation.Comment: Accepted for publication on ACM Computing Survey

Impact of soil properties on critical concentrations of cadmium, lead, copper, zinc and mercury in soil and soil solution in view of ecotoxicological effects

Concern about the input of metals to terrestrial ecosystems is related to (i) the ecotoxicological impact on soil organisms and plants (Bringmark et al. 1998; Palmborg et al. 1998) and also on aquatic organisms resulting from runoff to surface water and (ii) the uptake via food chains into animal tissues and products, which may result in health effects on animals and humans (Clark 1989). Effects on soil organisms, including microorganisms/macrofungi and soil fauna, such as nematodes and earthworms, are reduced species diversity, abundance, and biomass and changes in microbe-mediated processes (Bengtsson and Tranvik 1989; Giller et al. 1998; Vig et al. 2003). Effects on vascular plants include reduced development and growth of roots and shoots, elevated concentrations of starch and total sugar, decreased nutrient contents in foliar tissues, and decreased enzymatic activity (Prasad 1995; Das et al. 1997). A review of these phytotoxic effects is given by Balsberg-Påhlsson (1989). Effects on aquatic organisms, including algae, Crustacea, and fish, include effects on gill function (Sola et al. 1995), nervous systems (Baatrup 1991), and growth and reproduction rates (Mance 1987). Environmental quality standards or critical limits, often also denoted as Predicted No Effect Concentrations, or PNECs, for metals in soils and surface waters related to those effects serve as a guide in the environmental risk assessment process for those substances

From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing

Current efforts to recover the Neandertal and mammoth genomes by 454 DNA sequencing demonstrate the sensitivity of this technology. However, routine 454 sequencing applications still require microgram quantities of initial material. This is due to a lack of effective methods for quantifying 454 sequencing libraries, necessitating expensive and labour-intensive procedures when sequencing ancient DNA and other poor DNA samples. Here we report a 454 sequencing library quantification method based on quantitative PCR that effectively eliminates these limitations. We estimated both the molecule numbers and the fragment size distributions in sequencing libraries derived from Neandertal DNA extracts, SAGE ditags and bonobo genomic DNA, obtaining optimal sequencing yields without performing any titration runs. Using this method, 454 sequencing can routinely be performed from as little as 50 pg of initial material without titration runs, thereby drastically reducing costs while increasing the scope of sample throughput and protocol development on the 454 platform. The method should also apply to Illumina/Solexa and ABI/SOLiD sequencing, and should therefore help to widen the accessibility of all three platforms

The effect of Helicobacter pylori infection and eradication in patients with gastro-oesophageal reflux disease: A parallel-group, double-blind, placebo-controlled multicentre study

Objectives: This study aimed to resolve controversy regarding the effects of Helicobacter pylori eradication therapy and H. pylori infection in gastro-oesophageal reflux disease. Design: A randomized, double-blind, multicentre trial was performed in patients presenting with reflux symptoms. H. pylori-positive patients were randomized to receive either antibiotics or placebo for 7 days. H. pylori-negative patient controls received placebo. All received esomeprazole 20 mg b.d. for 7 days, followed by 40 mg o.d. to complete an 8-week course, and were followed up for 32 weeks by telephone. Results: In this study, 198/589 (34%) patients were H. pylori-positive and 113 H. pylori-negative patients served as controls. Baseline endoscopy revealed 63% Los Angeles grade 0A and 37% Los Angeles grade BCD oesophagitis with no difference between patient groups. Symptom improvement on esomeprazole was seen in 89%. H. pylori eradication was successful in 82%. H. pylori eradication had no effect on symptomatic relapse (hazard ratio 1.15, 95% CI 0.74–1.8; p = 0.5). Overall, H. pylori-positive patients had a lower probability of relapse compared to H. pylori-negative controls (hazard ratio 0.6, 95% CI 0.43–0.85; p = 0.004). Relapse hazard was modulated also by oesophagitis grade (BCD vs. 0A, hazard ratio 2.1, 95% CI 1.5–3.0). Conclusion: Relapse of gastro-oesophageal reflux disease symptoms after a course of high dose acid suppression took longer for H. pylori-positive patients than H. pylori-negative controls; however eradication therapy had no effect on the risk of relapse; ClincialTrials.gov number, NCT00574925

Insect assemblages attacking seeds and fruits in a rainforest in Thailand

Insect seed predators are important agents of mortality for tropical trees, but little is known about the impact of these herbivores in rainforests. During three years at Khao Chong (KHC) in southern Thailand we reared 17,555 insects from 343.2 kg or 39,252 seeds/fruits representing 357 liana and tree species. A commented list of the 243 insect species identified is provided, with details about their host plants. We observed that: (1) about 43% of identified species can be considered pests. Most were seed eaters, particularly on dry fruits. (2) About 19% of parasitoid species (all Opiinae) for which we could determine whether their primary insect host was a pest or not (all Bactrocera spp. breeding in fruits) can be considered beneficials. (3) The seeds/fruits of about 28% of the plant species in this forest were free of attack. Phyllanthaceae, Rubiaceae, and Meliaceae were attacked relatively infrequently; in contrast, Annonaceae, Fabaceae, Sapindaceae, and Myristicaceae were more heavily attacked. There was no apparent effect of plant phylogeny on rates of attack but heavily attacked tree species had larger basal area in the KHC plot than rarely attacked tree species. (4) Insects reared from fleshy fruits were more likely to exhibit relatively stable populations compared to insects reared from dry fruits, but this was not true of insects reared from dipterocarps, which appeared to have relatively stable populations throughout the study period. We tentatively conclude that insects feeding on seeds and fruits have little effect on observed levels of host abundance in this forest

Avoiding dative overgeneralisation errors: semantics, statistics or both?

Item does not contain fulltextHow do children eventually come to avoid the production of overgeneralisation errors, in particular, those involving the dative (e.g., *I said her "no")? The present study addressed this question by obtaining from adults and children (5-6, 9-10 years) judgements of well-formed and over-general datives with 301 different verbs (44 for children). A significant effect of pre-emption - whereby the use of a verb in the prepositional-object (PO)-dative construction constitutes evidence that double-object (DO)-dative uses are not permitted - was observed for every age group. A significant effect of entrenchment - whereby the use of a verb in any construction constitutes evidence that unattested dative uses are not permitted - was also observed for every age group, with both predictors also accounting for developmental change between ages 5-6 and 9-10 years. Adults demonstrated knowledge of a morphophonological constraint that prohibits Latinate verbs from appearing in the DO-dative construction (e.g., *I suggested her the trip). Verbs' semantic properties (supplied by independent adult raters) explained additional variance for all groups and developmentally, with the relative influence of narrow- vs broad-range semantic properties increasing with age. We conclude by outlining an account of the formation and restriction of argument-structure generalisations designed to accommodate these findings.26 p

Routine Inpatient HIV Testing System Increases Access to Pediatric HIV Care in sub-Saharan Africa

Routine HIV testing, called provider-initiated opt-out HIV testing and counseling (PITC), is recommended in African countries with high HIV prevalence. However, it is unknown whether PITC increases access to pediatric HIV care. In 2008 the Baylor International Pediatric AIDS Initiative implemented PITC (BIPAI-PITC) at a Malawian hospital. We sought to evaluate the influence of BIPAI-PITC, compared to non-routine HIV testing (NRT), on pediatric HIV care access

Vaccine delivery by penetratin: mechanism of antigen presentation by dendritic cells

Cell-penetrating peptides (CPP) or membrane-translocating peptides such as penetratin from Antennapedia homeodomain or TAT from human immunodeficiency virus are useful vectors for the delivery of protein antigens or their cytotoxic (Tc) or helper (Th) T cell epitopes to antigen-presenting cells. Mice immunized with CPP containing immunogens elicit antigen-specific Tc and/or Th responses and could be protected from tumor challenges. In the present paper, we investigate the mechanism of class I and class II antigen presentation of ovalbumin covalently linked to penetratin (AntpOVA) by bone marrow-derived dendritic cells with the use of biochemical inhibitors of various pathways of antigen processing and presentation. Results from our study suggested that uptake of AntpOVA is via a combination of energy-independent (membrane fusion) and energy-dependent pathways (endocytosis). Once internalized by either mechanism, multiple tap-dependent or independent antigen presentation pathways are accessed while not completely dependent on proteasomal processing but involving proteolytic trimming in the ER and Golgi compartments. Our study provides an understanding on the mechanism of antigen presentation mediated by CPP and leads to greater insights into future development of vaccine formulations