title: Heterogeneous Computing for Data Stream Mining

authors: Petko, Vladimir

subjects: data stream mining

abstract: Graphical Processing Units are de-facto standard for acceleration of data parallel tasks in high performance computing. They are widely used to accelerate batch machine learning algorithms. High-end discrete GPUs are characterized by a very high number of cores (thousands), high bandwidth memory optimized for the stream access and high power requirements. Integrated GPUs are characterized by a medium number of cores (hundreds), medium bandwidth memory shared with CPU optimized for the random access and low power  requirements. Data stream processing applications are often required to provide response within the limited time frame, operate on data in relatively small increments and have strict power requirements if deployed on the embedded devices. This work evaluates performance of integrated and discrete GPUs belonging to the same chip family on several variants of k-nearest neighbours algorithm over sliding window and stochastic gradient descent using OpenCL and novel Heterogeneous System Architecture platforms. We conclude that integrated GPUs provide a niche solution catering for to small work sizes that offers better power efficiency and simplicity of deployment.

text: Heterogeneous Computing for Data Stream Mining Graphical Processing Units are de-facto standard for acceleration of data parallel tasks in high performance computing. They are widely used to accelerate batch machine learning algorithms. High-end discrete GPUs are characterized by a very high number of cores (thousands), high bandwidth memory optimized for the stream access and high power requirements. Integrated GPUs are characterized by a medium number of cores (hundreds), medium bandwidth memory shared with CPU optimized for the random access and low power  requirements. Data stream processing applications are often required to provide response within the limited time frame, operate on data in relatively small increments and have strict power requirements if deployed on the embedded devices. This work evaluates performance of integrated and discrete GPUs belonging to the same chip family on several variants of k-nearest neighbours algorithm over sliding window and stochastic gradient descent using OpenCL and novel Heterogeneous System Architecture platforms. We conclude that integrated GPUs provide a niche solution catering for to small work sizes that offers better power efficiency and simplicity of deployment.

year: 2016

title: DNA adsorption by nanocrystalline allophane spherules and nanoaggregates, and implications for carbon sequestration in Andisols

authors: Huang, Yu-Tuan

subjects: Science & Technology

abstract: This study provides fundamental knowledge about the interaction of allophane, deoxyribonucleic acid (DNA), and organic matter in soils, and how allophane sequesters DNA. The adsorption capacities of salmon-sperm DNA on pure synthetic allophane (characterised morphologically and chemically) and on humic-acid-rich synthetic allophane were determined, and the resultant DNA–allophane complexes were characterised using synchrotron-radiation-derived P X-ray absorption near-edge fine structure (XANES) spectroscopy and infrared (IR) spectroscopy. The synthetic allophane adsorbed up to 34 μg mg⁻¹ of salmon-sperm DNA. However, the presence of humic acid significantly lowered the DNA uptake on the synthetic allophane to 3.5 μg mg⁻¹ by occupying the active sites on allophane so that DNA was repulsed. Both allophane and humic acid adsorbed DNA chemically through its phosphate groups. IR spectra for the allophane–DNA complex showed a chemical change of the Si–O–Al stretching of allophane after DNA adsorption, possibly because of the alteration of the steric distance of the allophane outer wall, or because of the precipitation of aluminium phosphate on allophane after DNA adsorption on it, or both. The aluminol groups of synthetic allophane almost completely reacted with additions of small amounts of DNA (~ 2–6 μg mg⁻¹ ), but the chemical adsorption of DNA on allophane simultaneously led to the formation of very porous allophane aggregates up to ~ 500 μm in diameter. The formation of the allophane nano- and microaggregates enabled up to 28 μg mg⁻¹ of DNA to be adsorbed (~ 80% of total) within spaces (pores) between allophane spherules and allophane nanoaggregates (as “physical adsorption”), giving a total of 34 μg mg⁻¹ of DNA adsorbed by the allophane. The stability of the allophane–DNA nano- and microaggregates likely prevents encapsulated DNA from exposure to oxidants, and DNA within small pores between allophane spherules and nanoaggregates may not be accessible to enzymes or microbes, hence enabling DNA protection and preservation in such materials. By implication, substantial organic carbon is therefore likely to be sequestered and protected in allophanic soils (Andisols) in the same way as demonstrated here for DNA, that is, predominantly by encapsulation within a tortuous network of nanopores and submicropores amidst stable nanoaggregates and microaggregates, rather than by chemisorption alone.

text: DNA adsorption by nanocrystalline allophane spherules and nanoaggregates, and implications for carbon sequestration in Andisols This study provides fundamental knowledge about the interaction of allophane, deoxyribonucleic acid (DNA), and organic matter in soils, and how allophane sequesters DNA. The adsorption capacities of salmon-sperm DNA on pure synthetic allophane (characterised morphologically and chemically) and on humic-acid-rich synthetic allophane were determined, and the resultant DNA–allophane complexes were characterised using synchrotron-radiation-derived P X-ray absorption near-edge fine structure (XANES) spectroscopy and infrared (IR) spectroscopy. The synthetic allophane adsorbed up to 34 μg mg⁻¹ of salmon-sperm DNA. However, the presence of humic acid significantly lowered the DNA uptake on the synthetic allophane to 3.5 μg mg⁻¹ by occupying the active sites on allophane so that DNA was repulsed. Both allophane and humic acid adsorbed DNA chemically through its phosphate groups. IR spectra for the allophane–DNA complex showed a chemical change of the Si–O–Al stretching of allophane after DNA adsorption, possibly because of the alteration of the steric distance of the allophane outer wall, or because of the precipitation of aluminium phosphate on allophane after DNA adsorption on it, or both. The aluminol groups of synthetic allophane almost completely reacted with additions of small amounts of DNA (~ 2–6 μg mg⁻¹ ), but the chemical adsorption of DNA on allophane simultaneously led to the formation of very porous allophane aggregates up to ~ 500 μm in diameter. The formation of the allophane nano- and microaggregates enabled up to 28 μg mg⁻¹ of DNA to be adsorbed (~ 80% of total) within spaces (pores) between allophane spherules and allophane nanoaggregates (as “physical adsorption”), giving a total of 34 μg mg⁻¹ of DNA adsorbed by the allophane. The stability of the allophane–DNA nano- and microaggregates likely prevents encapsulated DNA from exposure to oxidants, and DNA within small pores between allophane spherules and nanoaggregates may not be accessible to enzymes or microbes, hence enabling DNA protection and preservation in such materials. By implication, substantial organic carbon is therefore likely to be sequestered and protected in allophanic soils (Andisols) in the same way as demonstrated here for DNA, that is, predominantly by encapsulation within a tortuous network of nanopores and submicropores amidst stable nanoaggregates and microaggregates, rather than by chemisorption alone.

year: 2016-02-01

title: Equity of travel required to access first definitive surgery for liver or stomach cancer in New Zealand

authors: Gurney, Jason

subjects: Humans

abstract: In New Zealand, there are known disparities between the Indigenous Māori and the majority non-Indigenous European populations in access to cancer treatment, with resulting disparities in cancer survival. There is international evidence of ethnic disparities in the distance travelled to access cancer treatment; and as such, the aim of this paper was to examine the distance and time travelled to access surgical care between Māori and European liver and stomach cancer patients. We used national-level data and Geographic Information Systems (GIS) analysis to describe the distance travelled by patients to receive their first primary surgery for liver or stomach cancer, as well as the estimated time to travel this distance by road, and the surgical volume of hospitals performing these procedures. All cases of liver (ICD-10-AM 3rd edition code: C22) and stomach (C16) cancer that occurred in New Zealand (2007-2019) were drawn from the New Zealand Cancer Registry (liver cancer: 866 Māori, 2,460 European; stomach cancer: 953 Māori, 3,192 European), and linked to national inpatient hospitalisation records to examine access to surgery. We found that Māori on average travel 120km for liver cancer surgery, compared to around 60km for Europeans, while a substantial minority of both Māori and European liver cancer patients must travel more than 200km for their first primary liver surgery, and this situation appears worse for Māori (36% vs 29%; adj. OR 1.48, 95% CI 1.09-2.01). No such disparities were observed for stomach cancer. This contrast between cancers is likely driven by the centralisation of liver cancer surgery relative to stomach cancer. In order to support Māori to access liver cancer care, we recommend that additional support is provided to Māori patients (including prospective financial support), and that efforts are made to remotely provide those clinical services that can be decentralised.

text: Equity of travel required to access first definitive surgery for liver or stomach cancer in New Zealand In New Zealand, there are known disparities between the Indigenous Māori and the majority non-Indigenous European populations in access to cancer treatment, with resulting disparities in cancer survival. There is international evidence of ethnic disparities in the distance travelled to access cancer treatment; and as such, the aim of this paper was to examine the distance and time travelled to access surgical care between Māori and European liver and stomach cancer patients. We used national-level data and Geographic Information Systems (GIS) analysis to describe the distance travelled by patients to receive their first primary surgery for liver or stomach cancer, as well as the estimated time to travel this distance by road, and the surgical volume of hospitals performing these procedures. All cases of liver (ICD-10-AM 3rd edition code: C22) and stomach (C16) cancer that occurred in New Zealand (2007-2019) were drawn from the New Zealand Cancer Registry (liver cancer: 866 Māori, 2,460 European; stomach cancer: 953 Māori, 3,192 European), and linked to national inpatient hospitalisation records to examine access to surgery. We found that Māori on average travel 120km for liver cancer surgery, compared to around 60km for Europeans, while a substantial minority of both Māori and European liver cancer patients must travel more than 200km for their first primary liver surgery, and this situation appears worse for Māori (36% vs 29%; adj. OR 1.48, 95% CI 1.09-2.01). No such disparities were observed for stomach cancer. This contrast between cancers is likely driven by the centralisation of liver cancer surgery relative to stomach cancer. In order to support Māori to access liver cancer care, we recommend that additional support is provided to Māori patients (including prospective financial support), and that efforts are made to remotely provide those clinical services that can be decentralised.

year: 2022