Online solid phase extraction liquid chromatography tandem mass spectrometry (SPE-LC-MS/MS) method for the determination of sucralose in reclaimed and drinking waters and its photo degradation in natural waters from South Florida

Background Sucralose has gained popularity as a low calorie artificial sweetener worldwide. Due to its high stability and persistence, sucralose has shown widespread occurrence in environmental waters, at concentrations that could reach up to several μg/L. Previous studies have used time consuming sample preparation methods (offline solid phase extraction/derivatization) or methods with rather high detection limits (direct injection) for sucralose analysis. This study described a faster and sensitive analytical method for the determination of sucralose in environmental samples. Results An online SPE-LC–MS/MS method was developed, being capable to quantify sucralose in 12 minutes using only 10 mL of sample, with method detection limits (MDLs) of 4.5 ng/L, 8.5 ng/L and 45 ng/L for deionized water, drinking and reclaimed waters (1:10 diluted with deionized water), respectively. Sucralose was detected in 82% of the reclaimed water samples at concentrations reaching up to 18 μg/L. The monthly average for a period of one year was 9.1 ± 2.9 μg/L. The calculated mass loads per capita of sucralose discharged through WWTP effluents based on the concentrations detected in wastewaters in the U. S. is 5.0 mg/day/person. As expected, the concentrations observed in drinking water were much lower but still relevant reaching as high as 465 ng/L. In order to evaluate the stability of sucralose, photodegradation experiments were performed in natural waters. Significant photodegradation of sucralose was observed only in freshwater at 254 nm. Minimal degradation (<20%) was observed for all matrices under more natural conditions (350 nm or solar simulator). The only photolysis product of sucralose identified by high resolution mass spectrometry was a de-chlorinated molecule at m/z 362.0535, with molecular formula C12H20Cl2O8. Conclusions Online SPE LC-APCI/MS/MS developed in the study was applied to more than 100 environmental samples. Sucralose was frequently detected (>80%) indicating that the conventional treatment process employed in the sewage treatment plants is not efficient for its removal. Detection of sucralose in drinking waters suggests potential contamination of surface and ground waters sources with anthropogenic wastewater streams. Its high resistance to photodegradation, minimal sorption and high solubility indicate that sucralose could be a good tracer of anthropogenic wastewater intrusion into the environment.

A novel method for rapid and selective extraction of male DNA from rape kits using alkaline lysis and pressure cycling technology (PCT)

There is an increasing demand for DNA analysis because of the sensitivity of the method and the ability to uniquely identify and distinguish individuals with a high degree of certainty. But this demand has led to huge backlogs in evidence lockers since the current DNA extraction protocols require long processing time. The DNA analysis procedure becomes more complicated when analyzing sexual assault casework samples where the evidence contains more than one contributor. Additional processing to separate different cell types in order to simplify the final data interpretation further contributes to the existing cumbersome protocols. The goal of the present project is to develop a rapid and efficient extraction method that permits selective digestion of mixtures. ^ Selective recovery of male DNA was achieved with as little as 15 minutes lysis time upon exposure to high pressure under alkaline conditions. Pressure cycling technology (PCT) is carried out in a barocycler that has a small footprint and is semi-automated. Typically less than 10% male DNA is recovered using the standard extraction protocol for rape kits, almost seven times more male DNA was recovered from swabs using this novel method. Various parameters including instrument setting and buffer composition were optimized to achieve selective recovery of sperm DNA. Some developmental validation studies were also done to determine the efficiency of this method in processing samples exposed to various conditions that can affect the quality of the extraction and the final DNA profile. ^ Easy to use interface, minimal manual interference and the ability to achieve high yields with simple reagents in a relatively short time make this an ideal method for potential application in analyzing sexual assault samples.^

Towards next generation vertical search engines

As the Web evolves unexpectedly fast, information grows explosively. Useful resources become more and more difficult to find because of their dynamic and unstructured characteristics. A vertical search engine is designed and implemented towards a specific domain. Instead of processing the giant volume of miscellaneous information distributed in the Web, a vertical search engine targets at identifying relevant information in specific domains or topics and eventually provides users with up-to-date information, highly focused insights and actionable knowledge representation. As the mobile device gets more popular, the nature of the search is changing. So, acquiring information on a mobile device poses unique requirements on traditional search engines, which will potentially change every feature they used to have. To summarize, users are strongly expecting search engines that can satisfy their individual information needs, adapt their current situation, and present highly personalized search results. ^ In my research, the next generation vertical search engine means to utilize and enrich existing domain information to close the loop of vertical search engine's system that mutually facilitate knowledge discovering, actionable information extraction, and user interests modeling and recommendation. I investigate three problems in which domain taxonomy plays an important role, including taxonomy generation using a vertical search engine, actionable information extraction based on domain taxonomy, and the use of ensemble taxonomy to catch user's interests. As the fundamental theory, ultra-metric, dendrogram, and hierarchical clustering are intensively discussed. Methods on taxonomy generation using my research on hierarchical clustering are developed. The related vertical search engine techniques are practically used in Disaster Management Domain. Especially, three disaster information management systems are developed and represented as real use cases of my research work.^

Assessment of silicone polymer composites for the trace extraction of herbicides : a tool for environmental forensics

Passive samplers are not only a versatile tool to integrate environmental concentrations of pollutants, but also to avoid the use of live sentinel organisms for environmental monitoring. This study introduced the use of magnetic silicone polymer composites (Fe-PDMS) as passive sampling media to pre-concentrate a wide range of analytes from environmental settings. The composite samplers were assessed for their accumulation properties by performing lab experiments with two model herbicides (Atrazine and Irgarol 1051) and evaluated for their uptake properties from environmental settings (waters and sediments). The Fe-PDMS composites showed good accumulation of herbicides and pesticides from both freshwater and saltwater settings and the accumulation mechanism was positively correlated with the log Kow value of individual analytes. Results from the studies show that these composites could be easily used for a wide number of applications such as monitoring, cleanup, and/or bioaccumulation modeling, and as a non-intrusive and nondestructive monitoring tool for environmental forensic purposes.

A Novel Method for Rapid and Selective Extraction of Male DNA from Rape Kits using Alkaline Lysis and Pressure Cycling Technology (PCT)

There is an increasing demand for DNA analysis because of the sensitivity of the method and the ability to uniquely identify and distinguish individuals with a high degree of certainty. But this demand has led to huge backlogs in evidence lockers since the current DNA extraction protocols require long processing time. The DNA analysis procedure becomes more complicated when analyzing sexual assault casework samples where the evidence contains more than one contributor. Additional processing to separate different cell types in order to simplify the final data interpretation further contributes to the existing cumbersome protocols. The goal of the present project is to develop a rapid and efficient extraction method that permits selective digestion of mixtures. Selective recovery of male DNA was achieved with as little as 15 minutes lysis time upon exposure to high pressure under alkaline conditions. Pressure cycling technology (PCT) is carried out in a barocycler that has a small footprint and is semi-automated. Typically less than 10% male DNA is recovered using the standard extraction protocol for rape kits, almost seven times more male DNA was recovered from swabs using this novel method. Various parameters including instrument setting and buffer composition were optimized to achieve selective recovery of sperm DNA. Some developmental validation studies were also done to determine the efficiency of this method in processing samples exposed to various conditions that can affect the quality of the extraction and the final DNA profile. Easy to use interface, minimal manual interference and the ability to achieve high yields with simple reagents in a relatively short time make this an ideal method for potential application in analyzing sexual assault samples.

Towards Next Generation Vertical Search Engines

As the Web evolves unexpectedly fast, information grows explosively. Useful resources become more and more difficult to find because of their dynamic and unstructured characteristics. A vertical search engine is designed and implemented towards a specific domain. Instead of processing the giant volume of miscellaneous information distributed in the Web, a vertical search engine targets at identifying relevant information in specific domains or topics and eventually provides users with up-to-date information, highly focused insights and actionable knowledge representation. As the mobile device gets more popular, the nature of the search is changing. So, acquiring information on a mobile device poses unique requirements on traditional search engines, which will potentially change every feature they used to have. To summarize, users are strongly expecting search engines that can satisfy their individual information needs, adapt their current situation, and present highly personalized search results. In my research, the next generation vertical search engine means to utilize and enrich existing domain information to close the loop of vertical search engine's system that mutually facilitate knowledge discovering, actionable information extraction, and user interests modeling and recommendation. I investigate three problems in which domain taxonomy plays an important role, including taxonomy generation using a vertical search engine, actionable information extraction based on domain taxonomy, and the use of ensemble taxonomy to catch user's interests. As the fundamental theory, ultra-metric, dendrogram, and hierarchical clustering are intensively discussed. Methods on taxonomy generation using my research on hierarchical clustering are developed. The related vertical search engine techniques are practically used in Disaster Management Domain. Especially, three disaster information management systems are developed and represented as real use cases of my research work.

(Figure 1 and 2) Phosphorus pools in the investigated sediments quantified by SEDEX sequential extraction and distribution of recovered 33P spike between sedimentary P pools after incubation

Phosphorus is an essential nutrient for life. In the ocean, phosphorus burial regulates marine primary production**1, 2. Phosphorus is removed from the ocean by sedimentation of organic matter, and the subsequent conversion of organic phosphorus to phosphate minerals such as apatite, and ultimately phosphorite deposits**3, 4. Bacteria are thought to mediate these processes**5, but the mechanism of sequestration has remained unclear. Here, we present results from laboratory incubations in which we labelled organic-rich sediments from the Benguela upwelling system, Namibia, with a 33P-radiotracer, and tracked the fate of the phosphorus. We show that under both anoxic and oxic conditions, large sulphide-oxidizing bacteria accumulate 33P in their cells, and catalyse the nearly instantaneous conversion of phosphate to apatite. Apatite formation was greatest under anoxic conditions. Nutrient analyses of Namibian upwelling waters and sediments suggest that the rate of phosphate-to-apatite conversion beneath anoxic bottom waters exceeds the rate of phosphorus release during organic matter mineralization in the upper sediment layers. We suggest that bacterial apatite formation is a significant phosphorus sink under anoxic bottom-water conditions. Expanding oxygen minimum zones are projected in simulations of future climate change**6, potentially increasing sequestration of marine phosphate, and restricting marine productivity.

Machine learning classification of surgical pathology reports and chunk recognition for information extraction noise reduction

Background and aims: Machine learning techniques for the text mining of cancer-related clinical documents have not been sufficiently explored. Here some techniques are presented for the pre-processing of free-text breast cancer pathology reports, with the aim of facilitating the extraction of information relevant to cancer staging.

Materials and methods: The first technique was implemented using the freely available software RapidMiner to classify the reports according to their general layout: ‘semi-structured’ and ‘unstructured’. The second technique was developed using the open source language engineering framework GATE and aimed at the prediction of chunks of the report text containing information pertaining to the cancer morphology, the tumour size, its hormone receptor status and the number of positive nodes. The classifiers were trained and tested respectively on sets of 635 and 163 manually classified or annotated reports, from the Northern Ireland Cancer Registry.

Results: The best result of 99.4% accuracy – which included only one semi-structured report predicted as unstructured – was produced by the layout classifier with the k nearest algorithm, using the binary term occurrence word vector type with stopword filter and pruning. For chunk recognition, the best results were found using the PAUM algorithm with the same parameters for all cases, except for the prediction of chunks containing cancer morphology. For semi-structured reports the performance ranged from 0.97 to 0.94 and from 0.92 to 0.83 in precision and recall, while for unstructured reports performance ranged from 0.91 to 0.64 and from 0.68 to 0.41 in precision and recall. Poor results were found when the classifier was trained on semi-structured reports but tested on unstructured.

Conclusions: These results show that it is possible and beneficial to predict the layout of reports and that the accuracy of prediction of which segments of a report may contain certain information is sensitive to the report layout and the type of information sought.

The neurotoxin β-N-methylamino-L-alanine (BMAA) : Sources, bioaccumulation and extraction procedures

β-methylamino-L-alanine (BMAA) is a neurotoxin linked to neurodegeneration, which is manifested in the devastating human diseases amyotrophic lateral sclerosis, Alzheimer’s and Parkinson’s disease. This neurotoxin is known to be produced by almost all tested species within the cyanobacterial phylum including free living as well as the symbiotic strains. The global distribution of the BMAA producers ranges from a terrestrial ecosystem on the Island of Guam in the Pacific Ocean to an aquatic ecosystem in Northern Europe, the Baltic Sea, where annually massive surface blooms occur. BMAA had been shown to accumulate in the Baltic Sea food web, with highest levels in the bottom dwelling fish-species as well as in mollusks. One of the aims of this thesis was to test the bottom-dwelling bioaccumulation hypothesis by using a larger number of samples allowing a statistical evaluation. Hence, a large set of fish individuals from the lake Finjasjön, were caught and the BMAA concentrations in different tissues were related to the season of catching, fish gender, total weight and species. The results reveal that fish total weight and fish species were positively correlated with BMAA concentration in the fish brain. Therefore, significantly higher concentrations of BMAA in the brain were detected in plankti-benthivorous fish species and heavier (potentially older) individuals. Another goal was to investigate the potential production of BMAA by other phytoplankton organisms. Therefore, diatom cultures were investigated and confirmed to produce BMAA, even in higher concentrations than cyanobacteria. All diatom cultures studied during this thesis work were show to contain BMAA, as well as one dinoflagellate species. This might imply that the environmental spread of BMAA in aquatic ecosystems is even higher than previously thought. Earlier reports on the concentration of BMAA in different organisms have shown highly variable results and the methods used for quantification have been intensively discussed in the scientific community. In the most recent studies, liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the instrument of choice, due to its high sensitivity and selectivity. Even so, different studies show quite variable concentrations of BMAA. In this thesis, three of the most common BMAA extraction protocols were evaluated in order to find out if the extraction could be one of the sources of variability. It was found that the method involving precipitation of proteins using trichloroacetic acid gave the best performance, complying with all in-house validation criteria. However, extractions of diatom and cyanobacteria cultures with this validated method and quantified using LC-MS/MS still resulted in variable BMAA concentrations, which suggest that also biological reasons contribute to the discrepancies. The current knowledge on the environmental factors that can induce or reduce BMAA production is still limited. In cyanobacteria, production of BMAA was earlier shown to be negative correlated with nitrogen availability – both in laboratory cultures as well as in natural populations. Based on this observation, it was suggested that in unicellular non-diazotrophic cyanobacteria, BMAA might take part in nitrogen metabolism. In order to find out if BMAA has a similar role in diatoms, BMAA was added to two diatom species in culture, in concentrations corresponding to those earlier found in the diatoms. The results suggest that BMAA might induce a nitrogen starvation signal in diatoms, as was earlier observed in cyanobacteria. However, diatoms recover shortly by the extracellular presence of excreted ammonia. Thus, also in diatoms, BMAA might be involved in the nitrogen balance in the cell.

Automatically Evolving Rotation-invariant Texture Image Descriptors by Genetic Programming

In computer vision, training a model that performs classification effectively is highly dependent on the extracted features, and the number of training instances. Conventionally, feature detection and extraction are performed by a domain-expert who, in many cases, is expensive to employ and hard to find. Therefore, image descriptors have emerged to automate these tasks. However, designing an image descriptor still requires domain-expert intervention. Moreover, the majority of machine learning algorithms require a large number of training examples to perform well. However, labelled data is not always available or easy to acquire, and dealing with a large dataset can dramatically slow down the training process. In this paper, we propose a novel Genetic Programming based method that automatically synthesises a descriptor using only two training instances per class. The proposed method combines arithmetic operators to evolve a model that takes an image and generates a feature vector. The performance of the proposed method is assessed using six datasets for texture classification with different degrees of rotation, and is compared with seven domain-expert designed descriptors. The results show that the proposed method is robust to rotation, and has significantly outperformed, or achieved a comparable performance to, the baseline methods.

The governance of adaptation: choices, reasons, and effects. Introduction to the Special Feature

The governance of climate adaptation involves the collective efforts of multiple societal actors to address problems, or to reap the benefits, associated with impacts of climate change. Governing involves the creation of institutions, rules and organizations, and the selection of normative principles to guide problem solution and institution building. We argue that actors involved in governing climate change adaptation, as climate change governance regimes evolve, inevitably must engage in making choices, for instance on problem definitions, jurisdictional levels, on modes of governance and policy instruments, and on the timing of interventions. Yet little is known about how and why these choices are made in practice, and how such choices affect the outcomes of our efforts to govern adaptation. In this introduction we review the current state of evidence and the specific contribution of the articles published in this Special Feature, which are aimed at bringing greater clarity in these matters, and thereby informing both governance theory and practice. Collectively, the contributing papers suggest that the way issues are defined has important consequences for the support for governance interventions, and their effectiveness. The articles suggest that currently the emphasis in adaptation governance is on the local and regional levels, while underscoring the benefits of interventions and governance at higher jurisdictional levels in terms of visioning and scaling-up effective approaches. The articles suggest that there is a central role of government agencies in leading governance interventions to address spillover effects, to provide public goods, and to promote the long-term perspectives for planning. They highlight the issue of justice in the governance of adaptation showing how governance measures have wide distributional consequences, including the potential to amplify existing inequalities, access to resources, or generating new injustices through distribution of risks. For several of these findings, future research directions are suggested.

Discovery driven analysis on semi-structured text data

Discovery Driven Analysis (DDA) is a common feature of OLAP technology to analyze structured data. In essence, DDA helps analysts to discover anomalous data by highlighting 'unexpected' values in the OLAP cube. By giving indications to the analyst on what dimensions to explore, DDA speeds up the process of discovering anomalies and their causes. However, Discovery Driven Analysis (and OLAP in general) is only applicable on structured data, such as records in databases. We propose a system to extend DDA technology to semi-structured text documents, that is, text documents with a few structured data. Our system pipeline consists of two stages: first, the text part of each document is structured around user specified dimensions, using semi-PLSA algorithm; then, we adapt DDA to these fully structured documents, thus enabling DDA on text documents. We present some applications of this system in OLAP analysis and show how scalability issues are solved. Results show that our system can handle reasonable datasets of documents, in real time, without any need for pre-computation.

Development of a simple and fast “DNA extraction kit” for sea food identification and marine species

Seafood products fraud, the misrepresentation of them, have been discovered all around the world in different forms as false labeling, species substitution, short-weighting or over glazing in order to hide the correct identity, origin or weight of the seafood products. Due to the value of seafood products such as canned tuna, swordfish or grouper, these species are the subject of the commercial fraud is mainly there placement of valuable species with other little or no value species. A similar situation occurs with the shelled shrimp or shellfish that are reduced into pieces for the commercialization. Food fraud by species substitution is an emerging risk given the increasingly global food supply chain and the potential food safety issues. Economic food fraud is committed when food is deliberately placed on the market, for financial gain deceiving consumers (Woolfe, M. & Primrose, S. 2004). As a result of the increased demand and the globalization of the seafood supply, more fish species are encountered in the market. In this scenary, it becomes essential to unequivocally identify the species. The traditional taxonomy, based primarily on identification keys of species, has shown a number of limitations in the use of the distinctive features in many animal taxa, amplified when fish, crustacean or shellfish are commercially transformed. Many fish species show a similar texture, thus the certification of fish products is particularly important when fishes have undergone procedures which affect the overall anatomical structure, such as heading, slicing or filleting (Marko et al., 2004). The absence of morphological traits, a main characteristic usually used to identify animal species, represents a challenge and molecular identification methods are required. Among them, DNA-based methods are more frequently employed for food authentication (Lockley & Bardsley, 2000). In addition to food authentication and traceability, studies of taxonomy, population and conservation genetics as well as analysis of dietary habits and prey selection, also rely on genetic analyses including the DNA barcoding technology (Arroyave & Stiassny, 2014; Galimberti et al., 2013; Mafra, Ferreira, & Oliveira, 2008; Nicolé et al., 2012; Rasmussen & Morrissey, 2008), consisting in PCR amplification and sequencing of a COI mitochondrial gene specific region. The system proposed by P. Hebert et al. (2003) locates inside the mitochondrial COI gene (cytochrome oxidase subunit I) the bioidentification system useful in taxonomic identification of species (Lo Brutto et al., 2007). The COI region, used for genetic identification - DNA barcode - is short enough to allow, with the current technology, to decode sequence (the pairs of nucleotide bases) in a single step. Despite, this region only represents a tiny fraction of the mitochondrial DNA content in each cell, the COI region has sufficient variability to distinguish the majority of species among them (Biondo et al. 2016). This technique has been already employed to address the demand of assessing the actual identity and/or provenance of marketed products, as well as to unmask mislabelling and fraudulent substitutions, difficult to detect especially in manufactured seafood (Barbuto et al., 2010; Galimberti et al., 2013; Filonzi, Chiesa, Vaghi, & Nonnis Marzano, 2010). Nowadays,the research concerns the use of genetic markers to identify not only the species and/or varieties of fish, but also to identify molecular characters able to trace the origin and to provide an effective control tool forproducers and consumers as a supply chain in agreementwith local regulations.

Engraulis encrasicolus (Linnaeus, 1758): technical report about extraction and recognition of the digestive tract contents in early stages of the life cycle

The study of ichthyio-plankton stages and its relations with the environment and other organisms is therefore crucial for a correct use of fishery resources. In this context, the extraction and the analysis of the content of the digestive tract, is a key method for the identification of the diet in early larval stages, the determination of the resources they rely on and possibly a comparison with the diet of other species. Additionally this approach could be useful in determination on occurrence of species competition. This technique is preceded by the analysis of morphometric data (Blackith & Reyment, 1971; Marcus, 1990), that is the acquisition of quantitative variables measured from the morphology of the object of study. They are linear distances, count, angles and ratios. The subsequent application of multivariate statistical methods, aims to quantify the changes in morphological measures between and within groups, relating them to the type and size of prey and evaluate if some changes appear in food choices along the larvae growth.