title: Weka: practical machine learning tools and techniques with Java Implementations

authors: Witten, Ian H.

abstract: The Waikato Environment for Knowledge Analysis(Weka) is a comprehensive suite of Java class libraries that implement many state-of-the-art machine learning and data mining algorithms.

Weka is freely available on the World-Wide Weband accompanies a new text on data mining which documents and fully explains all the algorithms it contains. Applications written using the Weka class libraries can be run on anycomputer with a Web browsing capability.

text: Weka: practical machine learning tools and techniques with Java Implementations The Waikato Environment for Knowledge Analysis(Weka) is a comprehensive suite of Java class libraries that implement many state-of-the-art machine learning and data mining algorithms.

Weka is freely available on the World-Wide Weband accompanies a new text on data mining which documents and fully explains all the algorithms it contains. Applications written using the Weka class libraries can be run on anycomputer with a Web browsing capability.

year: 1999-11-22

title: Robust mathematical programming for natural resource modelling under parametric uncertainty

authors: Doole, Graeme J.

subjects: parameter uncertainty

abstract: Inaccurate specification of model coefficients can lead to false or distorted findings in modeling investigations of natural resource management. Hence, this paper outlines a decision framework for optimization problems in which only the bounded set of outcomes for uncertain parameters is known. These models can be solved with standard mathematical programming software and are no larger than their deterministic equivalent. The robust approach is contrasted against deterministic analysis and is demonstrated for two applications regarding the management of natural resources. Deterministic plans are infeasible in at least 40% of cases when parameters vary from their point estimates. Inclusion of robust constraints immunizes against this infeasibility, thereby removing errors arising from false certainty. Additionally, incorporation of bounded parameters in the objective function yields interval-valued sets containing potential outcomes. However, this increase in the general relevance of model output introduces some degree of suboptimality as deterministic plans are buffered to proactively account for potential variability. The cost of robustness increases with the simulated spread of uncertain coefficients but may be reduced through accounting for the uncertainty aversion of decision makers.

text: Robust mathematical programming for natural resource modelling under parametric uncertainty Inaccurate specification of model coefficients can lead to false or distorted findings in modeling investigations of natural resource management. Hence, this paper outlines a decision framework for optimization problems in which only the bounded set of outcomes for uncertain parameters is known. These models can be solved with standard mathematical programming software and are no larger than their deterministic equivalent. The robust approach is contrasted against deterministic analysis and is demonstrated for two applications regarding the management of natural resources. Deterministic plans are infeasible in at least 40% of cases when parameters vary from their point estimates. Inclusion of robust constraints immunizes against this infeasibility, thereby removing errors arising from false certainty. Additionally, incorporation of bounded parameters in the objective function yields interval-valued sets containing potential outcomes. However, this increase in the general relevance of model output introduces some degree of suboptimality as deterministic plans are buffered to proactively account for potential variability. The cost of robustness increases with the simulated spread of uncertain coefficients but may be reduced through accounting for the uncertainty aversion of decision makers.

year: 2010

title: In vitro cell culture to study microglial inflammation

authors: Newland, Julia

subjects: CNs

abstract: Inflammation of the central nervous system (CNS) characterised by release of cytokines such as tumour necrosis factor-alpha (TNF-a) and interleukin-1 (IL-1) is an event that is often detrimental to neuronal cells and is thought to contribute to the neuronal loss observed during neurodegeneration.
One objective of this study was to investigate the potential anti-inflammatory properties of kawakawa leaf extracts using in vitro model cell systems. Kawakawa leaf extracts anti-inflammatory properties have anecdotally been documented in traditional Maori medicinal practices (Rangoa). However, before this aspect could be carried out, experiments were undertaken to investigate the effects the kawakawa leaf extracts had on the growth rates of two mammalian cell lines (HeLa and THP-1 cells).
Interestingly, the growth assays showed that the extracts to have both a stimulatory and inhibitory effect on cell growth. Toxicity of cells can be categorised as either necrotic or apoptotic cell death. In this study, HeLa cells and THP-1 cells were incubated under standard growth conditions with various concentrations (10 to 100ug/ml) of Kawakawa leave extracts prepared at room temperature or 60OC.
Growth data as seen in figures 2 and 3 typically have a long lag phase before they start to reach exponential growth between days 4 and 5. The extract having the largest stimulatory effect on HeLa cells as shown by figure 6 was 25 ug/ml at 60OC and the largest inhibitory effect seen on HeLa cells was seen at 50 ug/ml RT shown by figure 6. The extract which has the largest stimulatory effect on THP-1 cells is 25 ug/ml 60OC as shown by figure 11 whereas the extract producing the largest inhibitory effect is 25 ug/ml RT.

Apoptotic and necrotic cell death mechanisms were examined by using in vitro biochemistry techniques. Assessments were largely made based on biochemical changes of HeLa cells and THP-1 cells post treatment of Kawakawa leave extracts.
Measurement of lactate dehydrogenase (LDH assays) in the growth media of cells that were shown to be growth inhibited during exposure to Kawakawa extracts indicated that the growth inhibition resulting from exposure to the extracts was not due to necrotic cell death processes. (ie that cells maintained their membrane integrity) When compared to the control, a lower amount of cytosolic LDH was seen in THP-1 cell lines. However, HeLa cell lines produced a high level of cytosolic LDH which may be due to mycoplasma contamination. On average, Kawakawa concentrations at 12.5ug/ml and 25ug/ml yielded less lysed cells percentage across both cell lines.
The demonstrated cell growth inhibition was unlikely to be due to necrosis and because of this it was decided to see if cell death was caused by mitochondrial processes that would further support apoptotic cell death. The biochemical assay MTT indirectly measures mitochondrial dehydrogenase activity in the presence of kawakawa leave extracts.
The MTT data illustrated mitochondrial impairment where HeLa cells exposed to Kawakawa 60OC concentrations 6.25 ug/ml and 12.5 ug/ml had the lowest average mitochondrial activity. THP-1 cells exposed to Kawakawa 60OC concentrations 12.5 ug/ml and 50 ug/ml had the lowest average mitochondrial activity.
The main results of this study include, the treatment of HeLa and THP-1 cells with kawakawa extracts demonstrated that cytotoxicity was not due to necrosis. The most interesting finding of this study is when kawakawa extracts inhibit cell growth there is no increase in LDH. This is suggestive that the cellular membrane remains intact when exposed to the extract.

text: In vitro cell culture to study microglial inflammation Inflammation of the central nervous system (CNS) characterised by release of cytokines such as tumour necrosis factor-alpha (TNF-a) and interleukin-1 (IL-1) is an event that is often detrimental to neuronal cells and is thought to contribute to the neuronal loss observed during neurodegeneration.
One objective of this study was to investigate the potential anti-inflammatory properties of kawakawa leaf extracts using in vitro model cell systems. Kawakawa leaf extracts anti-inflammatory properties have anecdotally been documented in traditional Maori medicinal practices (Rangoa). However, before this aspect could be carried out, experiments were undertaken to investigate the effects the kawakawa leaf extracts had on the growth rates of two mammalian cell lines (HeLa and THP-1 cells).
Interestingly, the growth assays showed that the extracts to have both a stimulatory and inhibitory effect on cell growth. Toxicity of cells can be categorised as either necrotic or apoptotic cell death. In this study, HeLa cells and THP-1 cells were incubated under standard growth conditions with various concentrations (10 to 100ug/ml) of Kawakawa leave extracts prepared at room temperature or 60OC.
Growth data as seen in figures 2 and 3 typically have a long lag phase before they start to reach exponential growth between days 4 and 5. The extract having the largest stimulatory effect on HeLa cells as shown by figure 6 was 25 ug/ml at 60OC and the largest inhibitory effect seen on HeLa cells was seen at 50 ug/ml RT shown by figure 6. The extract which has the largest stimulatory effect on THP-1 cells is 25 ug/ml 60OC as shown by figure 11 whereas the extract producing the largest inhibitory effect is 25 ug/ml RT.

Apoptotic and necrotic cell death mechanisms were examined by using in vitro biochemistry techniques. Assessments were largely made based on biochemical changes of HeLa cells and THP-1 cells post treatment of Kawakawa leave extracts.
Measurement of lactate dehydrogenase (LDH assays) in the growth media of cells that were shown to be growth inhibited during exposure to Kawakawa extracts indicated that the growth inhibition resulting from exposure to the extracts was not due to necrotic cell death processes. (ie that cells maintained their membrane integrity) When compared to the control, a lower amount of cytosolic LDH was seen in THP-1 cell lines. However, HeLa cell lines produced a high level of cytosolic LDH which may be due to mycoplasma contamination. On average, Kawakawa concentrations at 12.5ug/ml and 25ug/ml yielded less lysed cells percentage across both cell lines.
The demonstrated cell growth inhibition was unlikely to be due to necrosis and because of this it was decided to see if cell death was caused by mitochondrial processes that would further support apoptotic cell death. The biochemical assay MTT indirectly measures mitochondrial dehydrogenase activity in the presence of kawakawa leave extracts.
The MTT data illustrated mitochondrial impairment where HeLa cells exposed to Kawakawa 60OC concentrations 6.25 ug/ml and 12.5 ug/ml had the lowest average mitochondrial activity. THP-1 cells exposed to Kawakawa 60OC concentrations 12.5 ug/ml and 50 ug/ml had the lowest average mitochondrial activity.
The main results of this study include, the treatment of HeLa and THP-1 cells with kawakawa extracts demonstrated that cytotoxicity was not due to necrosis. The most interesting finding of this study is when kawakawa extracts inhibit cell growth there is no increase in LDH. This is suggestive that the cellular membrane remains intact when exposed to the extract.

year: 2016