Kinetics of the urea–urease clock reaction with urease immobilized in hydrogel beads

Feedback driven by enzyme catalyzed reactions occurs widely in biology and has been well characterized in single celled organisms such as yeast. There are still few examples of robust enzyme oscillators in vitro that might be used to study nonlinear dynamical behavior. One of the simplest is the urea–urease reaction that displays autocatalysis driven by the increase in pH accompanying the production of ammonia. A clock reaction was obtained from low to high pH in batch reactor and bistability and oscillations were reported in a continuous flow rector. However, the oscillations were found to be irreproducible and one contributing factor may be the lack of stability of the enzyme in solution at room temperature. Here, we investigated the effect of immobilizing urease in thiol-poly(ethylene glycol) acrylate (PEGDA) hydrogel beads, prepared using emulsion polymerization, on the urea–urease reaction. The resultant mm-sized beads were found to reproduce the pH clock and, under the conditions employed here, the stability of the enzyme was increased from hours to days

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

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

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

Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing

Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated (PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias

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

Is there scope for community health nurses to address lifestyle risk factors? the community nursing SNAP trial

<p>Abstract</p> <p>Background</p> <p>This paper examines the opportunity and need for lifestyle interventions for patients attending generalist community nursing services in Australia. This will help determine the scope for risk factor management within community health care by generalist community nurses (GCNs).</p> <p>Methods</p> <p>This was a quasi-experimental study conducted in four generalist community nursing services in NSW, Australia. Prior to service contacts, clients were offered a computer-assisted telephone interview to collect baseline data on socio-demographics, health conditions, smoking status, physical activity levels, alcohol consumption, height and weight, fruit and vegetable intake and 'readiness-to-change' for lifestyle risk factors.</p> <p>Results</p> <p>804 clients participated (a response rate of 34.1%). Participants had higher rates of obesity (40.5% vs 32.1%) and higher prevalence of multiple risk factors (40.4% vs 29.5%) than in the general population. Few with a SNAPW (Smoking-Nutrition-Alcohol-Physical-Activity-Weight) risk factor had received advice or referral in the previous 3 months. The proportion of clients identified as at risk and who were open to change (i.e. contemplative, in preparation or in action phase) were 65.0% for obese/overweight; 73.8% for smokers; 48.2% for individuals with high alcohol intake; 83.5% for the physically inactive and 59.0% for those with poor nutrition.</p> <p>Conclusions</p> <p>There was high prevalence of lifestyle risk factors. Although most were ready to change, few clients recalled having received any recent lifestyle advice. This suggests that there is considerable scope for intervention by GCNs. The results of this trial will shed light on how best to implement the lifestyle risk factor management in routine practice.</p

The mediterranean dietary pattern and breast cancer risk in Greek-Cypriot women: a case-control study

Background: Diet has long been suspected to impact on breast cancer risk. In this study we evaluated whether the degree of adherence to a Mediterranean diet pattern modifies breast cancer risk amongst Greek-Cypriot women. Methods: Subjects included 935 cases and 817 controls, all participating in the MASTOS case-control study in Cyprus. The study was approved by the Cyprus National Bioethics Committee. Information on dietary intakes was collected using an interviewer administered 32-item Food Frequency Questionnaire. Information on demographic, anthropometric, lifestyle, and other confounding factors was also collected. Adherence to the Mediterranean Diet pattern was assessed using two a-priory defined diet scores. In addition, dietary patterns specific to our population were derived using Principal Component Analysis (PCA). Logistic regression models were used to assess the association between the dietary patters and breast cancer risk. Results: There was no association with breast cancer risk for either score, however, higher consumptions of vegetables, fish and olive oil, were independently associated with decreased risk. In addition, the PCA derived component which included vegetables, fruit, fish and legumes was shown to significantly reduce risk of breast cancer (ORs across quartiles of increasing levels of consumption: 0.89 95%CI: 0.65-1.22, 0.64 95%CI: 0.47-0.88, 0.67 95%CI: 0.49-0.92, P trend < 0.0001), even after adjustment for relevant confounders. Conclusions: Our results suggest that adherence to a diet pattern rich in vegetables, fish, legumes and olive oil may favorably influence the risk of breast cancer. This study is the first investigation of dietary effects on breast cancer risk in Cyprus, a country whose population has traditionally adhered to the Mediterranean diet