McLean et al. (2009) (henceforth MFC09) claim that the El Niño-Southern Oscillation (ENSO), as re... more McLean et al. (2009) (henceforth MFC09) claim that the El Niño-Southern Oscillation (ENSO), as represented by the Southern Oscillation Index (SOI), accounts for as much as 72% of the global tropospheric temperature anomaly and an even higher 81% of this anomaly in the tropics. They conclude that the SOI is a "dominant and consistent influence on mean global temperatures," "and perhaps recent trends in global temperatures." However, their analysis is inappropriate in a number of ways and overstates the influence of ENSO on the climate system. This comment first briefly reviews what is understood about the influence of ENSO on global temperatures and then shows that the analysis of MFC09 greatly overestimates the correlation between temperature anomalies and the SOI by inflating the power in the 2-6 year time window while filtering out variability on longer and shorter time scales. The suggestion in their conclusions that ENSO may be a major contributor to recent trends in global temperature is not supported by their analysis or any physical theory presented in their paper, especially as the analysis method itself eliminates the influence of trends on the purported correlations.
ABSTRACT As USArray peregrinates across the western United States, the volumes of data it produce... more ABSTRACT As USArray peregrinates across the western United States, the volumes of data it produces offer unique opportunities for seismic imaging. Constraining structures on a range of length scales and their physical and chemical causes is a prerequisite for understanding the relationship between near surface and deeper mantle processes. We produce 3-D models of P-wavespeed variations in the mantle from linearized inversion of travel time residuals from USArray combined with the global EHB catalog. We perform global inversions, but an adaptable parameterization enhances resolution in regions where more data are available. This adaptability allows us to create an internally consistent model while at the same time reaching a resolution in the western United States nearly equivalent to that of regional tomography studies. The addition of USArray data results in a significant improvement of spatial resolution of upper mantle structure beneath the western United States. This will help us understand, for example, the structural transitions from the central craton to the tectonic domains further west, the deep structure of the Cascadia subduction zone, and the relationship between the Yellowstone hotspot and processes deeper in the mantle. Model updates will be made available to the community and will also be useful as starting models for higher resolution wave equation tomography studies.
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to org... more The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.
The Journal of the Acoustical Society of America, 2015
An acoustic survey of secondary schools in England has been undertaken. Room acoustic parameters ... more An acoustic survey of secondary schools in England has been undertaken. Room acoustic parameters and background noise levels were measured in 185 unoccupied spaces in 13 schools to provide information on the typical acoustic environment of secondary schools. The unoccupied acoustic and noise data were correlated with various physical characteristics of the spaces. Room height and the amount of glazing were related to the unoccupied reverberation time and therefore need to be controlled to reduce reverberation to suitable levels for teaching and learning. Further analysis of the unoccupied data showed that the introduction of legislation relating to school acoustics in England and Wales in 2003 approximately doubled the number of school spaces complying with current standards. Noise levels were also measured during 274 lessons to examine typical levels generated during teaching activities in secondary schools and to investigate the influence of acoustic design on working noise levels in the classroom. Comparison of unoccupied and occupied data showed that unoccupied acoustic conditions affect the noise levels occurring during lessons. They were also related to the time spent in disruption to the lessons (e.g., students talking or shouting) and so may also have an impact upon student behavior in the classroom.
Earth’s atmosphere is made up of 78% nitrogen and 21% oxygen. It is therefore highly oxidising bu... more Earth’s atmosphere is made up of 78% nitrogen and 21% oxygen. It is therefore highly oxidising but the oxygen only acts as the main source of the more reactive molecules and free radicals that provide the atmosphere’s real oxidising power. These are formed almost entirely by photochemistry and many involve coupling between ozone and water vapour, the influence of which
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to org... more The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.
Adjuvant chemotherapy improves patient survival rates after resection for pancreatic adenocarcino... more Adjuvant chemotherapy improves patient survival rates after resection for pancreatic adenocarcinoma, but the optimal duration and time to initiate chemotherapy is unknown. Patients with pancreatic ductal adenocarcinoma treated within the international, phase III, European Study Group for Pancreatic Cancer-3 (version 2) study were included if they had been randomly assigned to chemotherapy. Overall survival analysis was performed on an intention-to-treat basis, retaining patients in their randomized groups, and adjusting the overall treatment effect by known prognostic variables as well as the start time of chemotherapy. There were 985 patients, of whom 486 (49%) received gemcitabine and 499 (51%) received fluorouracil; 675 patients (68%) completed all six cycles of chemotherapy (full course) and 293 patients (30%) completed one to five cycles. Lymph node involvement, resection margins status, tumor differentiation, and completion of therapy were all shown by multivariable Cox regression to be independent survival factors. Overall survival favored patients who completed the full six courses of treatment versus those who did not (hazard ratio [HR], 0.516; 95% CI, 0.443 to 0.601; P < .001). Time to starting chemotherapy did not influence overall survival rates for the full study population (HR, 0.985; 95% CI, 0.956 to 1.015). Chemotherapy start time was an important survival factor only for the subgroup of patients who did not complete therapy, in favor of later treatment (P < .001). Completion of all six cycles of planned adjuvant chemotherapy rather than early initiation was an independent prognostic factor after resection for pancreatic adenocarcinoma. There seems to be no difference in outcome if chemotherapy is delayed up to 12 weeks, thus allowing adequate time for postoperative recovery.
British Journal of Mathematical and Statistical Psychology, 1991
ABSTRACT Wide use has been made of multidimensional scaling (MDS) techniques since the pioneering... more ABSTRACT Wide use has been made of multidimensional scaling (MDS) techniques since the pioneering papers of Shepard and Kruskal. In the main, dissimilarities used in the various MDS techniques are derived for pairs of objects or stimuli. This is termed 2-way, 1-mode data, meaning pairs of objects within a single set are considered. Some MDS techniques are designed for 3-way or even higher, and for 2-mode, 3-mode or more. One such example is the CANDECOMP model which can deal with n-way, m-mode data where 3≤n≤7 and 2≤m≤7. This model considers n-tuples of objects at a time, selecting these from m different sets.To date there are no models which consider n-way, 1-mode data, where n≥3. An attempt is made in this paper to cater for this situation by an extension of the Shepard-Kruskal approach to non-metric multidimensional scaling which deals with dissimilarities defined for three or more objects. A computer program has been written using the new model to produce a configuration in Euclidean space to represent the objects. Some historical voting data and some artificial data are then analysed.
Volcanic plumes are highly chemically reactive; both in the hot, near-vent plume, and also at amb... more Volcanic plumes are highly chemically reactive; both in the hot, near-vent plume, and also at ambient temperatures in the downwind plume, as the volcanic gases and aerosol disperse into the background atmosphere. In particular, DOAS (Differential Optical Absortpion Spectroscopy) observations have identified BrO (Bromine Monoxide) in several volcanic plumes degassing into the troposphere. These observations are explained by rapid in-plume
future changes. Reported results include new estimates of radiative forcing based on extensive mo... more future changes. Reported results include new estimates of radiative forcing based on extensive model studies of chemically active climate compounds like O 3 , and of particles inducing both direct and indirect effects. Through EU projects like ACCENT, QUANTIFY, and the AeroCom project, extensive studies on regional and sector-wise differences in the impact on atmospheric distribution are performed. Studies have shown that land-based emissions have a different effect on climate than ship and aircraft emissions, and different measures are needed to reduce the climate impact. Several areas where climate change can affect the tropospheric oxidation process and the chemical composition are identified. This can take place through enhanced stratospheric-tropospheric exchange of ozone, more frequent periods with stable conditions favoring pollution build up over industrial areas, enhanced temperature induced biogenic emissions, methane releases from permafrost thawing, and enhanced concentration through reduced biospheric uptake. During the last 5-10 years, new observational data have been made available and used for model validation and the study of atmospheric processes. Although there are significant uncertainties in the modeling of composition changes, access to new observational data has improved modeling capability. Emission scenarios for the coming decades have a large uncertainty range, in particular with respect to regional trends, leading to a significant uncertainty range in estimated regional composition changes and climate impact.
McLean et al. (2009) (henceforth MFC09) claim that the El Niño-Southern Oscillation (ENSO), as re... more McLean et al. (2009) (henceforth MFC09) claim that the El Niño-Southern Oscillation (ENSO), as represented by the Southern Oscillation Index (SOI), accounts for as much as 72% of the global tropospheric temperature anomaly and an even higher 81% of this anomaly in the tropics. They conclude that the SOI is a "dominant and consistent influence on mean global temperatures," "and perhaps recent trends in global temperatures." However, their analysis is inappropriate in a number of ways and overstates the influence of ENSO on the climate system. This comment first briefly reviews what is understood about the influence of ENSO on global temperatures and then shows that the analysis of MFC09 greatly overestimates the correlation between temperature anomalies and the SOI by inflating the power in the 2-6 year time window while filtering out variability on longer and shorter time scales. The suggestion in their conclusions that ENSO may be a major contributor to recent trends in global temperature is not supported by their analysis or any physical theory presented in their paper, especially as the analysis method itself eliminates the influence of trends on the purported correlations.
ABSTRACT As USArray peregrinates across the western United States, the volumes of data it produce... more ABSTRACT As USArray peregrinates across the western United States, the volumes of data it produces offer unique opportunities for seismic imaging. Constraining structures on a range of length scales and their physical and chemical causes is a prerequisite for understanding the relationship between near surface and deeper mantle processes. We produce 3-D models of P-wavespeed variations in the mantle from linearized inversion of travel time residuals from USArray combined with the global EHB catalog. We perform global inversions, but an adaptable parameterization enhances resolution in regions where more data are available. This adaptability allows us to create an internally consistent model while at the same time reaching a resolution in the western United States nearly equivalent to that of regional tomography studies. The addition of USArray data results in a significant improvement of spatial resolution of upper mantle structure beneath the western United States. This will help us understand, for example, the structural transitions from the central craton to the tectonic domains further west, the deep structure of the Cascadia subduction zone, and the relationship between the Yellowstone hotspot and processes deeper in the mantle. Model updates will be made available to the community and will also be useful as starting models for higher resolution wave equation tomography studies.
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to org... more The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.
The Journal of the Acoustical Society of America, 2015
An acoustic survey of secondary schools in England has been undertaken. Room acoustic parameters ... more An acoustic survey of secondary schools in England has been undertaken. Room acoustic parameters and background noise levels were measured in 185 unoccupied spaces in 13 schools to provide information on the typical acoustic environment of secondary schools. The unoccupied acoustic and noise data were correlated with various physical characteristics of the spaces. Room height and the amount of glazing were related to the unoccupied reverberation time and therefore need to be controlled to reduce reverberation to suitable levels for teaching and learning. Further analysis of the unoccupied data showed that the introduction of legislation relating to school acoustics in England and Wales in 2003 approximately doubled the number of school spaces complying with current standards. Noise levels were also measured during 274 lessons to examine typical levels generated during teaching activities in secondary schools and to investigate the influence of acoustic design on working noise levels in the classroom. Comparison of unoccupied and occupied data showed that unoccupied acoustic conditions affect the noise levels occurring during lessons. They were also related to the time spent in disruption to the lessons (e.g., students talking or shouting) and so may also have an impact upon student behavior in the classroom.
Earth’s atmosphere is made up of 78% nitrogen and 21% oxygen. It is therefore highly oxidising bu... more Earth’s atmosphere is made up of 78% nitrogen and 21% oxygen. It is therefore highly oxidising but the oxygen only acts as the main source of the more reactive molecules and free radicals that provide the atmosphere’s real oxidising power. These are formed almost entirely by photochemistry and many involve coupling between ozone and water vapour, the influence of which
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to org... more The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.
Adjuvant chemotherapy improves patient survival rates after resection for pancreatic adenocarcino... more Adjuvant chemotherapy improves patient survival rates after resection for pancreatic adenocarcinoma, but the optimal duration and time to initiate chemotherapy is unknown. Patients with pancreatic ductal adenocarcinoma treated within the international, phase III, European Study Group for Pancreatic Cancer-3 (version 2) study were included if they had been randomly assigned to chemotherapy. Overall survival analysis was performed on an intention-to-treat basis, retaining patients in their randomized groups, and adjusting the overall treatment effect by known prognostic variables as well as the start time of chemotherapy. There were 985 patients, of whom 486 (49%) received gemcitabine and 499 (51%) received fluorouracil; 675 patients (68%) completed all six cycles of chemotherapy (full course) and 293 patients (30%) completed one to five cycles. Lymph node involvement, resection margins status, tumor differentiation, and completion of therapy were all shown by multivariable Cox regression to be independent survival factors. Overall survival favored patients who completed the full six courses of treatment versus those who did not (hazard ratio [HR], 0.516; 95% CI, 0.443 to 0.601; P < .001). Time to starting chemotherapy did not influence overall survival rates for the full study population (HR, 0.985; 95% CI, 0.956 to 1.015). Chemotherapy start time was an important survival factor only for the subgroup of patients who did not complete therapy, in favor of later treatment (P < .001). Completion of all six cycles of planned adjuvant chemotherapy rather than early initiation was an independent prognostic factor after resection for pancreatic adenocarcinoma. There seems to be no difference in outcome if chemotherapy is delayed up to 12 weeks, thus allowing adequate time for postoperative recovery.
British Journal of Mathematical and Statistical Psychology, 1991
ABSTRACT Wide use has been made of multidimensional scaling (MDS) techniques since the pioneering... more ABSTRACT Wide use has been made of multidimensional scaling (MDS) techniques since the pioneering papers of Shepard and Kruskal. In the main, dissimilarities used in the various MDS techniques are derived for pairs of objects or stimuli. This is termed 2-way, 1-mode data, meaning pairs of objects within a single set are considered. Some MDS techniques are designed for 3-way or even higher, and for 2-mode, 3-mode or more. One such example is the CANDECOMP model which can deal with n-way, m-mode data where 3≤n≤7 and 2≤m≤7. This model considers n-tuples of objects at a time, selecting these from m different sets.To date there are no models which consider n-way, 1-mode data, where n≥3. An attempt is made in this paper to cater for this situation by an extension of the Shepard-Kruskal approach to non-metric multidimensional scaling which deals with dissimilarities defined for three or more objects. A computer program has been written using the new model to produce a configuration in Euclidean space to represent the objects. Some historical voting data and some artificial data are then analysed.
Volcanic plumes are highly chemically reactive; both in the hot, near-vent plume, and also at amb... more Volcanic plumes are highly chemically reactive; both in the hot, near-vent plume, and also at ambient temperatures in the downwind plume, as the volcanic gases and aerosol disperse into the background atmosphere. In particular, DOAS (Differential Optical Absortpion Spectroscopy) observations have identified BrO (Bromine Monoxide) in several volcanic plumes degassing into the troposphere. These observations are explained by rapid in-plume
future changes. Reported results include new estimates of radiative forcing based on extensive mo... more future changes. Reported results include new estimates of radiative forcing based on extensive model studies of chemically active climate compounds like O 3 , and of particles inducing both direct and indirect effects. Through EU projects like ACCENT, QUANTIFY, and the AeroCom project, extensive studies on regional and sector-wise differences in the impact on atmospheric distribution are performed. Studies have shown that land-based emissions have a different effect on climate than ship and aircraft emissions, and different measures are needed to reduce the climate impact. Several areas where climate change can affect the tropospheric oxidation process and the chemical composition are identified. This can take place through enhanced stratospheric-tropospheric exchange of ozone, more frequent periods with stable conditions favoring pollution build up over industrial areas, enhanced temperature induced biogenic emissions, methane releases from permafrost thawing, and enhanced concentration through reduced biospheric uptake. During the last 5-10 years, new observational data have been made available and used for model validation and the study of atmospheric processes. Although there are significant uncertainties in the modeling of composition changes, access to new observational data has improved modeling capability. Emission scenarios for the coming decades have a large uncertainty range, in particular with respect to regional trends, leading to a significant uncertainty range in estimated regional composition changes and climate impact.
Uploads
Papers by T. Cox