title: A data-driven approach to predict suspended-sediment reference concentration under non-breaking waves

authors: Oehler, Francois

subjects: Boosted Regression Trees

abstract: Using a detailed set of hydrodynamic and suspended-sediment observations, we developed data-driven algorithms based on Boosted Regression Trees and Artificial Neural Networks to predict suspended-sediment reference (near-bed) concentration using water depth, wave-orbital semi-excursion, wave period and bed-sediment grainsize as inputs. With one exception, the response of the data-driven algorithms was physically sound; the exception was the response to water depth. Outside of the range covered by the data, predictor performance could not be assessed and is not necessarily reliable. Boosted Regression Trees provide the best predictor of suspended-sediment reference concentration and have a clear explanatory power. Artificial Neural Networks provide slightly poorer predictions. Although the response of the latter is more difficult to interpret, they can be more easily included in numerical models simulating larger (in space) and longer (in time) morphodynamic behavior. Within the range of variability provided by the measurements, these algorithms outperform conventional process-based predictors.

text: A data-driven approach to predict suspended-sediment reference concentration under non-breaking waves Using a detailed set of hydrodynamic and suspended-sediment observations, we developed data-driven algorithms based on Boosted Regression Trees and Artificial Neural Networks to predict suspended-sediment reference (near-bed) concentration using water depth, wave-orbital semi-excursion, wave period and bed-sediment grainsize as inputs. With one exception, the response of the data-driven algorithms was physically sound; the exception was the response to water depth. Outside of the range covered by the data, predictor performance could not be assessed and is not necessarily reliable. Boosted Regression Trees provide the best predictor of suspended-sediment reference concentration and have a clear explanatory power. Artificial Neural Networks provide slightly poorer predictions. Although the response of the latter is more difficult to interpret, they can be more easily included in numerical models simulating larger (in space) and longer (in time) morphodynamic behavior. Within the range of variability provided by the measurements, these algorithms outperform conventional process-based predictors.

year: 2012

title: Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry

authors: McKenzie, Joanna Leigh

subjects: Mycobacteria

abstract: The VapBC toxin-antitoxin (TA) family is the largest of nine identified TA families. The toxin, VapC, is a metal-dependent ribonuclease that is inhibited by its cognate antitoxin, VapB. Although the VapBCs are the largest TA family, little is known about their biological roles. Here we describe a new general method for the overexpression and purification of toxic VapC proteins and subsequent determination of their RNase sequence-specificity. Functional VapC was isolated by expression of the nontoxic VapBC complex, followed by removal of the labile antitoxin (VapB) using limited trypsin digestion. We have then developed a sensitive and robust method for determining VapC ribonuclease sequence-specificity. This technique employs the use of Pentaprobes as substrates for VapC. These are RNA sequences encoding every combination of five bases. We combine the RNase reaction with MALDI-TOF MS to detect and analyze the cleavage products and thus determine the RNA cut sites. Successful MALDI-TOF MS analysis of RNA fragments is acutely dependent on sample preparation methods. The sequencespecificity of four VapC proteins from two different organisms (VapCPAE0151 and VapCPAE2754 from Pyrobaculum aerophilum, and VapCRv0065 and VapCRv0617 from Mycobacterium tuberculosis) was successfully determined using the described strategy. This rapid and sensitive method can be applied to determine the sequence-specificity of VapC ribonucleases along with other RNA interferases (such as MazF) from a range of organisms. Published by Cold Spring Harbor Laboratory Press.

text: Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry The VapBC toxin-antitoxin (TA) family is the largest of nine identified TA families. The toxin, VapC, is a metal-dependent ribonuclease that is inhibited by its cognate antitoxin, VapB. Although the VapBCs are the largest TA family, little is known about their biological roles. Here we describe a new general method for the overexpression and purification of toxic VapC proteins and subsequent determination of their RNase sequence-specificity. Functional VapC was isolated by expression of the nontoxic VapBC complex, followed by removal of the labile antitoxin (VapB) using limited trypsin digestion. We have then developed a sensitive and robust method for determining VapC ribonuclease sequence-specificity. This technique employs the use of Pentaprobes as substrates for VapC. These are RNA sequences encoding every combination of five bases. We combine the RNase reaction with MALDI-TOF MS to detect and analyze the cleavage products and thus determine the RNA cut sites. Successful MALDI-TOF MS analysis of RNA fragments is acutely dependent on sample preparation methods. The sequencespecificity of four VapC proteins from two different organisms (VapCPAE0151 and VapCPAE2754 from Pyrobaculum aerophilum, and VapCRv0065 and VapCRv0617 from Mycobacterium tuberculosis) was successfully determined using the described strategy. This rapid and sensitive method can be applied to determine the sequence-specificity of VapC ribonucleases along with other RNA interferases (such as MazF) from a range of organisms. Published by Cold Spring Harbor Laboratory Press.

year: 2012

title: A game of slides and ladders: Māori health providers and funders

authors: Masters-Awatere, Bridgette

abstract: Devolution of government responsibility after the neo-liberal reforms of the 1980s, and the re-orientation of health services towards public health in the 1990s, created an opportunity for Māori to take control of their own health outcomes through the delivery of culturally relevant and appropriate services. By 2000 “By Maori, For Maori” service provision had burst forth as the preferred approach with Māori. While grappling with the tendency of government agencies to fund services based on pre-existing health output criteria, Māori service providers were “walking on egg shells” under the constant threat of losing their funding. Currentcontracting does not capture the extent of the work done by Māori providers to serve precariat families. Nor does it adequately acknowledge, validate or value indigenous approaches to health and wellbeing. Instead, narrow, administratively demanding and difficult to interpret contracts threaten the provision of culturally relevant services. This chapter talks about some of the creative and insightful ways Māori service providers manage contrasting cultural and contractual expectations.

text: A game of slides and ladders: Māori health providers and funders Devolution of government responsibility after the neo-liberal reforms of the 1980s, and the re-orientation of health services towards public health in the 1990s, created an opportunity for Māori to take control of their own health outcomes through the delivery of culturally relevant and appropriate services. By 2000 “By Maori, For Maori” service provision had burst forth as the preferred approach with Māori. While grappling with the tendency of government agencies to fund services based on pre-existing health output criteria, Māori service providers were “walking on egg shells” under the constant threat of losing their funding. Currentcontracting does not capture the extent of the work done by Māori providers to serve precariat families. Nor does it adequately acknowledge, validate or value indigenous approaches to health and wellbeing. Instead, narrow, administratively demanding and difficult to interpret contracts threaten the provision of culturally relevant services. This chapter talks about some of the creative and insightful ways Māori service providers manage contrasting cultural and contractual expectations.

year: 2017