title: Positive, Negative, or Neutral: Learning an Expanded Opinion Lexicon from Emoticon-annotated Tweets

authors: Bravo-Marquez, Felipe

subjects: Machine learning

abstract: We present a supervised framework for expanding an opinion lexicon for tweets. The lexicon contains part-of-speech (POS) disambiguated entries with a three-dimensional probability distribution for positive, negative, and neutral polarities. To obtain this distribution using machine learning, we propose word-level attributes based on POS tags and information calculated from streams of emoticon annotated tweets. Our experimental results show that our method outperforms the three-dimensional word-level polarity classification performance obtained by semantic orientation, a state-of-the-art measure for establishing world-level sentiment.

text: Positive, Negative, or Neutral: Learning an Expanded Opinion Lexicon from Emoticon-annotated Tweets We present a supervised framework for expanding an opinion lexicon for tweets. The lexicon contains part-of-speech (POS) disambiguated entries with a three-dimensional probability distribution for positive, negative, and neutral polarities. To obtain this distribution using machine learning, we propose word-level attributes based on POS tags and information calculated from streams of emoticon annotated tweets. Our experimental results show that our method outperforms the three-dimensional word-level polarity classification performance obtained by semantic orientation, a state-of-the-art measure for establishing world-level sentiment.

year: 2015

title: Selenium as a Modulator of Efficacy and Toxicity of Chemotherapy and Radiation

authors: Lobb, Richard

subjects: selenium cancer

abstract: Selenium (Se) is an essential trace mineral required in maintaining health in humans. Recent research has demonstrated that Se shows promise as an agent that can reduce the harmful side-effects of chemotherapy (CT) and radiotherapy (RT), while not compromising the effectiveness of treatment. Clinical evaluations using varying doses of Se have demonstrated a significant reduction in toxicity of CT and RT. Se supplementation appears to mediate its biological effects through four main mechanisms: Se treatment promotes the death of malignant cells, but not normal cells, through the differential effects on the endoplasmic reticulum stress response; it inhibits hypoxia-induced angiogenesis which is required by tumours for their blood supply; it enhances DNA repair in normal but not malignant cells; and it reverses cellular resistance to some cytotoxic drugs. The objectives of this thesis were to evaluate the biological characteristics of the differential impact of a Se compound, methylseleninic acid (MSA), on malignant and non-malignant human cells and how that modulates the effects of cisplatin chemotherapy and/or radiation. In parallel with this, similar evaluations were undertaken in patients receiving a Se compound or placebo in conjunction with cisplatin and radiation for head and neck squamous cell carcinoma (HNSCC). MSA induced differential effects in peripheral blood mononuclear cells (PBMC) obtained from healthy individuals compared to the monocytic leukaemia THP-1 cell-line. While MSA did not change PBMC viability, it reduced that of THP-1 cells in a concentration-dependent manner. Furthermore, MSA treatment enhanced the cytotoxicity of CT and RT toward THP-1 cells without compromising the survival of PBMC. This increased sensitivity in THP-1 cells is likely to be related to significantly reduced levels of intracellular glutathione (GSH) in response to MSA. In contrast, GSH levels in PBMC rose substantially in response to MSA. Assessment of ER stress response proteins revealed that pro-survival proteins (GRP78, phospho-eIF2α, and spliced XBP-1) were upregulated in PBMC in response to MSA treatment. The malignant THP-1 cells had high levels of pro-survival proteins at baseline, which increased to a variable degree, especially caspase-8, in response to MSA. Putative pharmacodynamic markers of biological activity of Se were evaluated in plasma samples and PBMC from HNSCC patients in a randomised, placebo-controlled, double-blind phase II trial. Patients were treated with a 7-week radical course of concurrent cisplatin and RT (CRT) and were randomised to receive either selenomethionine (SLM) or matching placebo for 11 weeks, starting a week prior to CRT treatment. Because the trial is not yet complete, treatment allocation remains blinded and thus the pharmacodynamic results according to treatment with SLM or placebo cannot be made at the time of writing this thesis. However, markers of angiogenesis and the selenoprotein glutathione peroxidise 3 were measured and shown to significantly change during the course of treatment in a patient-specific manner. Lastly, ER stress markers were shown to be detected in PBMC obtained from patients during treatment. Se compounds differentially affect non-malignant and malignant cells. This results in increased therapeutic efficacy of cisplatin and RT targeting malignant cells. These effects appear to be mediated, at least in part, by modulation of intracellular GSH and ER stress response proteins

text: Selenium as a Modulator of Efficacy and Toxicity of Chemotherapy and Radiation Selenium (Se) is an essential trace mineral required in maintaining health in humans. Recent research has demonstrated that Se shows promise as an agent that can reduce the harmful side-effects of chemotherapy (CT) and radiotherapy (RT), while not compromising the effectiveness of treatment. Clinical evaluations using varying doses of Se have demonstrated a significant reduction in toxicity of CT and RT. Se supplementation appears to mediate its biological effects through four main mechanisms: Se treatment promotes the death of malignant cells, but not normal cells, through the differential effects on the endoplasmic reticulum stress response; it inhibits hypoxia-induced angiogenesis which is required by tumours for their blood supply; it enhances DNA repair in normal but not malignant cells; and it reverses cellular resistance to some cytotoxic drugs. The objectives of this thesis were to evaluate the biological characteristics of the differential impact of a Se compound, methylseleninic acid (MSA), on malignant and non-malignant human cells and how that modulates the effects of cisplatin chemotherapy and/or radiation. In parallel with this, similar evaluations were undertaken in patients receiving a Se compound or placebo in conjunction with cisplatin and radiation for head and neck squamous cell carcinoma (HNSCC). MSA induced differential effects in peripheral blood mononuclear cells (PBMC) obtained from healthy individuals compared to the monocytic leukaemia THP-1 cell-line. While MSA did not change PBMC viability, it reduced that of THP-1 cells in a concentration-dependent manner. Furthermore, MSA treatment enhanced the cytotoxicity of CT and RT toward THP-1 cells without compromising the survival of PBMC. This increased sensitivity in THP-1 cells is likely to be related to significantly reduced levels of intracellular glutathione (GSH) in response to MSA. In contrast, GSH levels in PBMC rose substantially in response to MSA. Assessment of ER stress response proteins revealed that pro-survival proteins (GRP78, phospho-eIF2α, and spliced XBP-1) were upregulated in PBMC in response to MSA treatment. The malignant THP-1 cells had high levels of pro-survival proteins at baseline, which increased to a variable degree, especially caspase-8, in response to MSA. Putative pharmacodynamic markers of biological activity of Se were evaluated in plasma samples and PBMC from HNSCC patients in a randomised, placebo-controlled, double-blind phase II trial. Patients were treated with a 7-week radical course of concurrent cisplatin and RT (CRT) and were randomised to receive either selenomethionine (SLM) or matching placebo for 11 weeks, starting a week prior to CRT treatment. Because the trial is not yet complete, treatment allocation remains blinded and thus the pharmacodynamic results according to treatment with SLM or placebo cannot be made at the time of writing this thesis. However, markers of angiogenesis and the selenoprotein glutathione peroxidise 3 were measured and shown to significantly change during the course of treatment in a patient-specific manner. Lastly, ER stress markers were shown to be detected in PBMC obtained from patients during treatment. Se compounds differentially affect non-malignant and malignant cells. This results in increased therapeutic efficacy of cisplatin and RT targeting malignant cells. These effects appear to be mediated, at least in part, by modulation of intracellular GSH and ER stress response proteins

year: 2011

title: Boat electrofishing surveys of fish populations in the Ohau Channel in 2011 and 2012

authors: Hicks, Brendan J.

abstract: The aim of the survey was to provide on-going monitoring of the fish communities and abundance in the Ohau Channel, especially fish species that are taonga to Maori (eels, goldfish, and koura). In the current study we present the findings from the fifth and sixth years of sampling (2011 and 2012) in view of previous surveys using boat electrofishing in the Ohau Channel.

We used the University of Waikato’s 4.5 m-long, aluminium-hulled electrofishing boat to catch a total of 399 fish (29.4 kg) from 10 sites in 2011 (2,420 linear m, 9,680 m² area) and 301 fish (12.8 kg) at 11 sites in 2012 (3,625 linear m, 14,500 m² area). Koura and 7 fish species were present in both years, with common bully the most abundant in 2011 and common smelt the most abundant in 2012. Common smelt were more abundant in 2012 (131 fish) than in 2011 (39 fish). Goldfish were most abundant at sites in the lower channel, especially at site 7.

As reflected in total numbers, common bullies had the highest densities of any fish species in 2011 (up to 7.4 fish 100 m⁻²), the majority of which were taken from edge habitats at sites 4, 5 and site 7. In 2012, common bully abundance was much reduced. However, despite the lower bully densities in 2012, mean bully biomass was higher in 2012 (1.00 g m⁻²) than in 2011 (0.04 g m⁻²) because bullies were smaller in 2011.

Common smelt had variable densities, the largest number of which was found in and around the excavated side branch at site 7 edge habitats (up to 14.7 fish 100 m⁻²) below the weir (site 1).

Mean density of rainbow trout in the Ohau Channel was similar in both years (0.27 fish 100 m⁻² in 2011,0.24 fish 100 m⁻² in 2012). Mean biomass of rainbow trout was much greater in 2012 (0.69 g m⁻² in 2011, 11.2 g m⁻² in 2012). Goldfish densities were greater in 2012, partly because goldfish at site 7 were targeted in 2012, and mean biomass was correspondingly greater (0.48 g m⁻² in 2011, 47.7 g m⁻² in 2012). Site 7 had 282 g m⁻² of goldfish biomass in 2012.

Catch per unit effort (CPUE) for common bullies in 2011 was twice that in 2012, reflecting lower densities in 2012. Common smelt CPUE in 2012, however, was 5 times greater than in 2011. Despite the much higher biomass of goldfish in 2012, CPUE was much the same.
The increased goldfish biomass in 2012 arose because of targeted fishing in the excavated side branch, which clearly offers good habitat for goldfish. In 2012, the first shortfin eel encountered in these surveys was caught. The abundance of common bully appears to have a clear trend of reducing abundance since these surveys started in 2007. The cause of this is not apparent, and not accounted for by water clarity expressed as black disk (BD) distance or water conductivity (Table 7). Poor water clarity can reduce the efficiency of electrofishing, but BD was greater in 2012 than in 2011. It is possible that smelt abundance has declined too, but the relatively inefficient sampling resulting from boat electrofishing must be considered. Independent verification is required.

text: Boat electrofishing surveys of fish populations in the Ohau Channel in 2011 and 2012 The aim of the survey was to provide on-going monitoring of the fish communities and abundance in the Ohau Channel, especially fish species that are taonga to Maori (eels, goldfish, and koura). In the current study we present the findings from the fifth and sixth years of sampling (2011 and 2012) in view of previous surveys using boat electrofishing in the Ohau Channel.

We used the University of Waikato’s 4.5 m-long, aluminium-hulled electrofishing boat to catch a total of 399 fish (29.4 kg) from 10 sites in 2011 (2,420 linear m, 9,680 m² area) and 301 fish (12.8 kg) at 11 sites in 2012 (3,625 linear m, 14,500 m² area). Koura and 7 fish species were present in both years, with common bully the most abundant in 2011 and common smelt the most abundant in 2012. Common smelt were more abundant in 2012 (131 fish) than in 2011 (39 fish). Goldfish were most abundant at sites in the lower channel, especially at site 7.

As reflected in total numbers, common bullies had the highest densities of any fish species in 2011 (up to 7.4 fish 100 m⁻²), the majority of which were taken from edge habitats at sites 4, 5 and site 7. In 2012, common bully abundance was much reduced. However, despite the lower bully densities in 2012, mean bully biomass was higher in 2012 (1.00 g m⁻²) than in 2011 (0.04 g m⁻²) because bullies were smaller in 2011.

Common smelt had variable densities, the largest number of which was found in and around the excavated side branch at site 7 edge habitats (up to 14.7 fish 100 m⁻²) below the weir (site 1).

Mean density of rainbow trout in the Ohau Channel was similar in both years (0.27 fish 100 m⁻² in 2011,0.24 fish 100 m⁻² in 2012). Mean biomass of rainbow trout was much greater in 2012 (0.69 g m⁻² in 2011, 11.2 g m⁻² in 2012). Goldfish densities were greater in 2012, partly because goldfish at site 7 were targeted in 2012, and mean biomass was correspondingly greater (0.48 g m⁻² in 2011, 47.7 g m⁻² in 2012). Site 7 had 282 g m⁻² of goldfish biomass in 2012.

Catch per unit effort (CPUE) for common bullies in 2011 was twice that in 2012, reflecting lower densities in 2012. Common smelt CPUE in 2012, however, was 5 times greater than in 2011. Despite the much higher biomass of goldfish in 2012, CPUE was much the same.
The increased goldfish biomass in 2012 arose because of targeted fishing in the excavated side branch, which clearly offers good habitat for goldfish. In 2012, the first shortfin eel encountered in these surveys was caught. The abundance of common bully appears to have a clear trend of reducing abundance since these surveys started in 2007. The cause of this is not apparent, and not accounted for by water clarity expressed as black disk (BD) distance or water conductivity (Table 7). Poor water clarity can reduce the efficiency of electrofishing, but BD was greater in 2012 than in 2011. It is possible that smelt abundance has declined too, but the relatively inefficient sampling resulting from boat electrofishing must be considered. Independent verification is required.

year: 2013