Time-series regression models to study the short-term effects of environmental factors on health

Time series regression models are especially suitable in epidemiology for evaluating short-term effects of time-varying exposures on health. The problem is that potential for confounding in time series regression is very high. Thus, it is important that trend and seasonality are properly accounted for. Our paper reviews the statistical models commonly used in time-series regression methods, specially allowing for serial correlation, make them potentially useful for selected epidemiological purposes. In particular, we discuss the use of time-series regression for counts using a wide range Generalised Linear Models as well as Generalised Additive Models. In addition, recently critical points in using statistical software for GAM were stressed, and reanalyses of time series data on air pollution and health were performed in order to update already published. Applications are offered through an example on the relationship between asthma emergency admissions and photochemical air pollutants

Evaluation of two soil carbon models using two Kenyan long term experimental datasets

RothC and Century are two of the most widely used soil organic matter (SOM) models. However there are few examples of specific parameterisation of these models for environmental conditions in East Africa. The aim of this study was therefore, to evaluate the ability of RothC and the Century to estimate changes in soil organic carbon (SOC) resulting from varying land use/management practices for the climate and soil conditions found in Kenya. The study used climate, soils and crop data from a long term experiment (1976-2001) carried out at The Kabete site at The Kenya National Agricultural Research Laboratories (NARL, located in a semi-humid region) and data from a 13 year experiment carried out in Machang'a (Embu District, located in a semi-arid region). The NARL experiment included various fertiliser (0, 60 and 120 kg of N and P2O5 ha(-1)), farmyard manure (FYM - 5 and 10 t ha(-1)) and plant residue treatments, in a variety of combinations. The Machang'a experiment involved a fertiliser (51 kg N ha(-1)) and a FYM (0, 5 and 10 t ha(-1)) treatment with both monocropping and intercropping. At Kabete both models showed a fair to good fit to measured data, although Century simulations for treatments with high levels of FYM were better than those without. At the Machang'a site with monocrops, both models showed a fair to good fit to measured data for all treatments. However, the fit of both models (especially RothC) to measured data for intercropping treatments at Machang'a was much poorer. Further model development for intercrop systems is recommended. Both models can be useful tools in soil C Predictions, provided time series of measured soil C and crop production data are available for validating model performance against local or regional agricultural crops. (C) 2007 Elsevier B.V. All rights reserved.

Can climate models capture the structure of extratropical cyclones?

Composites of wind speeds, equivalent potential temperature, mean sea level pressure, vertical velocity, and relative humidity have been produced for the 100 most intense extratropical cyclones in the Northern Hemisphere winter for the 40-yr ECMWF Re-Analysis (ERA-40) and the high resolution global environment model (HiGEM). Features of conceptual models of cyclone structure—the warm conveyor belt, cold conveyor belt, and dry intrusion—have been identified in the composites from ERA-40 and compared to HiGEM. Such features can be identified in the composite fields despite the smoothing that occurs in the compositing process. The surface features and the three-dimensional structure of the cyclones in HiGEM compare very well with those from ERA-40. The warm conveyor belt is identified in the temperature and wind fields as a mass of warm air undergoing moist isentropic uplift and is very similar in ERA-40 and HiGEM. The rate of ascent is lower in HiGEM, associated with a shallower slope of the moist isentropes in the warm sector. There are also differences in the relative humidity fields in the warm conveyor belt. In ERA-40, the high values of relative humidity are strongly associated with the moist isentropic uplift, whereas in HiGEM these are not so strongly associated. The cold conveyor belt is identified as rearward flowing air that undercuts the warm conveyor belt and produces a low-level jet, and is very similar in HiGEM and ERA-40. The dry intrusion is identified in the 500-hPa vertical velocity and relative humidity. The structure of the dry intrusion compares well between HiGEM and ERA-40 but the descent is weaker in HiGEM because of weaker along-isentrope flow behind the composite cyclone. HiGEM’s ability to represent the key features of extratropical cyclone structure can give confidence in future predictions from this model.

Linking bees and flowers: How do floral communities structure pollinator communities?

Pollinators provide essential ecosystem services, and declines in some pollinator communities around the world have been reported. Understanding the fundamental components defining these communities is essential if conservation and restoration are to be successful. We examined the structure of plant-pollinator communities in a dynamic Mediterranean landscape, comprising a mosaic of post-fire regenerating habitats, and which is a recognized global hotspot for bee diversity. Each community was characterized by a highly skewed species abundance distribution, with a few dominant and many rare bee species, and was consistent with a log series model indicating that a few environmental factors govern the community. Floral community composition, the quantity and quality of forage resources present, and the geographic locality organized bee communities at various levels: (1) The overall structure of the bee community (116 species), as revealed through ordination, was dependent upon nectar resource diversity (defined as the variety of nectar volume-concentration combinations available), the ratio of pollen to nectar energy, floral diversity, floral abundance, and post-fire age. (2) Bee diversity, measured as species richness, was closely linked to floral diversity (especially of annuals), nectar resource diversity, and post-fire age of the habitat. (3) The abundance of the most common species was primarily related to post-fire age, grazing intensity, and nesting substrate availability. Ordination models based on age-characteristic post-fire floral community structure explained 39-50% of overall variation observed in bee community structure. Cluster analysis showed that all the communities shared a high degree of similarity in their species composition (27-59%); however, the geographical location of sites also contributed a smaller but significant component to bee community structure. We conclude that floral resources act in specific and previously unexplored ways to modulate the diversity of the local geographic species pool, with specific disturbance factors, superimposed upon these patterns, mainly affecting the dominant species.

Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments

MOTIVATION: The accurate prediction of the quality of 3D models is a key component of successful protein tertiary structure prediction methods. Currently, clustering or consensus based Model Quality Assessment Programs (MQAPs) are the most accurate methods for predicting 3D model quality; however they are often CPU intensive as they carry out multiple structural alignments in order to compare numerous models. In this study, we describe ModFOLDclustQ - a novel MQAP that compares 3D models of proteins without the need for CPU intensive structural alignments by utilising the Q measure for model comparisons. The ModFOLDclustQ method is benchmarked against the top established methods in terms of both accuracy and speed. In addition, the ModFOLDclustQ scores are combined with those from our older ModFOLDclust method to form a new method, ModFOLDclust2, that aims to provide increased prediction accuracy with negligible computational overhead. RESULTS: The ModFOLDclustQ method is competitive with leading clustering based MQAPs for the prediction of global model quality, yet it is up to 150 times faster than the previous version of the ModFOLDclust method at comparing models of small proteins (<60 residues) and over 5 times faster at comparing models of large proteins (>800 residues). Furthermore, a significant improvement in accuracy can be gained over the previous clustering based MQAPs by combining the scores from ModFOLDclustQ and ModFOLDclust to form the new ModFOLDclust2 method, with little impact on the overall time taken for each prediction. AVAILABILITY: The ModFOLDclustQ and ModFOLDclust2 methods are available to download from: http://www.reading.ac.uk/bioinf/downloads/ CONTACT: l.j.mcguffin@reading.ac.uk.

Describing long-term trends in precipitation using generalized additive models

With the current concern over climate change, descriptions of how rainfall patterns are changing over time can be useful. Observations of daily rainfall data over the last few decades provide information on these trends. Generalized linear models are typically used to model patterns in the occurrence and intensity of rainfall. These models describe rainfall patterns for an average year but are more limited when describing long-term trends, particularly when these are potentially non-linear. Generalized additive models (GAMS) provide a framework for modelling non-linear relationships by fitting smooth functions to the data. This paper describes how GAMS can extend the flexibility of models to describe seasonal patterns and long-term trends in the occurrence and intensity of daily rainfall using data from Mauritius from 1962 to 2001. Smoothed estimates from the models provide useful graphical descriptions of changing rainfall patterns over the last 40 years at this location. GAMS are particularly helpful when exploring non-linear relationships in the data. Care is needed to ensure the choice of smooth functions is appropriate for the data and modelling objectives. (c) 2008 Elsevier B.V. All rights reserved.

Report of the 2010 assessment of the scientific assessment panel: future ozone and its impact on surface UV

SCIENTIFIC SUMMARY Globally averaged total column ozone has declined over recent decades due to the release of ozone-depleting substances (ODSs) into the atmosphere. Now, as a result of the Montreal Protocol, ozone is expected to recover from the effects of ODSs as ODS abundances decline in the coming decades. However, a number of factors in addition to ODSs have led to and will continue to lead to changes in ozone. Discriminating between the causes of past and projected ozone changes is necessary, not only to identify the progress in ozone recovery from ODSs, but also to evaluate the effectiveness of climate and ozone protection policy options. Factors Affecting Future Ozone and Surface Ultraviolet Radiation • At least for the next few decades, the decline of ODSs is expected to be the major factor affecting the anticipated increase in global total column ozone. However, several factors other than ODS will affect the future evolution of ozone in the stratosphere. These include changes in (i) stratospheric circulation and temperature due to changes in long-lived greenhouse gas (GHG) abundances, (ii) stratospheric aerosol loading, and (iii) source gases of highly reactive stratospheric hydrogen and nitrogen compounds. Factors that amplify the effects of ODSs on ozone (e.g., stratospheric aerosols) will likely decline in importance as ODSs are gradually eliminated from the atmosphere. • Increases in GHG emissions can both positively and negatively affect ozone. Carbon dioxide (CO2)-induced stratospheric cooling elevates middle and upper stratospheric ozone and decreases the time taken for ozone to return to 1980 levels, while projected GHG-induced increases in tropical upwelling decrease ozone in the tropical lower stratosphere and increase ozone in the extratropics. Increases in nitrous oxide (N2O) and methane (CH4) concentrations also directly impact ozone chemistry but the effects are different in different regions. • The Brewer-Dobson circulation (BDC) is projected to strengthen over the 21st century and thereby affect ozone amounts. Climate models consistently predict an acceleration of the BDC or, more specifically, of the upwelling mass flux in the tropical lower stratosphere of around 2% per decade as a consequence of GHG abundance increases. A stronger BDC would decrease the abundance of tropical lower stratospheric ozone, increase poleward transport of ozone, and could reduce the atmospheric lifetimes of long-lived ODSs and other trace gases. While simulations showing faster ascent in the tropical lower stratosphere to date are a robust feature of chemistry-climate models (CCMs), this has not been confirmed by observations and the responsible mechanisms remain unclear. • Substantial ozone losses could occur if stratospheric aerosol loading were to increase in the next few decades, while halogen levels are high. Stratospheric aerosol increases may be caused by sulfur contained in volcanic plumes entering the stratosphere or from human activities. The latter might include attempts to geoengineer the climate system by enhancing the stratospheric aerosol layer. The ozone losses mostly result from enhanced heterogeneous chemistry on stratospheric aerosols. Enhanced aerosol heating within the stratosphere also leads to changes in temperature and circulation that affect ozone. • Surface ultraviolet (UV) levels will not be affected solely by ozone changes but also by the effects of climate change and by air quality change in the troposphere. These tropospheric effects include changes in clouds, tropospheric aerosols, surface reflectivity, and tropospheric sulfur dioxide (SO2) and nitrogen dioxide (NO2). The uncertainties in projections of these factors are large. Projected increases in tropospheric ozone are more certain and may lead to reductions in surface erythemal (“sunburning”) irradiance of up to 10% by 2100. Changes in clouds may lead to decreases or increases in surface erythemal irradiance of up to 15% depending on latitude. Expected Future Changes in Ozone Full ozone recovery from the effects of ODSs and return of ozone to historical levels are not synonymous. In this chapter a key target date is chosen to be 1980, in part to retain the connection to previous Ozone Assessments. Noting, however, that decreases in ozone may have occurred in some regions of the atmosphere prior to 1980, 1960 return dates are also reported. The projections reported on in this chapter are taken from a recent compilation of CCM simulations. The ozone projections, which also form the basis for the UV projections, are limited in their representativeness of possible futures since they mostly come from CCM simulations based on a single GHG emissions scenario (scenario A1B of Emissions Scenarios. A Special Report of Working Group III of the Intergovernmental Panel on Climate Change, Cambridge University Press, 2000) and a single ODS emissions scenario (adjusted A1 of the previous (2006) Ozone Assessment). Throughout this century, the vertical, latitudinal, and seasonal structure of the ozone distribution will be different from what it was in 1980. For this reason, ozone changes in different regions of the atmosphere are considered separately. • The projections of changes in ozone and surface clear-sky UV are broadly consistent with those reported on in the 2006 Assessment. • The capability of making projections and attribution of future ozone changes has been improved since the 2006 Assessment. Use of CCM simulations from an increased number of models extending through the entire period of ozone depletion and recovery from ODSs (1960–2100) as well as sensitivity simulations have allowed more robust projections of long-term changes in the stratosphere and of the relative contributions of ODSs and GHGs to those changes. • Global annually averaged total column ozone is projected to return to 1980 levels before the middle of the century and earlier than when stratospheric halogen loading returns to 1980 levels. CCM projections suggest that this early return is primarily a result of GHG-induced cooling of the upper stratosphere because the effects of circulation changes on tropical and extratropical ozone largely cancel. Global (90°S–90°N) annually averaged total column ozone will likely return to 1980 levels between 2025 and 2040, well before the return of stratospheric halogens to 1980 levels between 2045 and 2060. • Simulated changes in tropical total column ozone from 1960 to 2100 are generally small. The evolution of tropical total column ozone in models depends on the balance between upper stratospheric increases and lower stratospheric decreases. The upper stratospheric increases result from declining ODSs and a slowing of ozone destruction resulting from GHG-induced cooling. Ozone decreases in the lower stratosphere mainly result from an increase in tropical upwelling. From 1960 until around 2000, a general decline is simulated, followed by a gradual increase to values typical of 1980 by midcentury. Thereafter, although total column ozone amounts decline slightly again toward the end of the century, by 2080 they are no longer expected to be affected by ODSs. Confidence in tropical ozone projections is compromised by the fact that simulated decreases in column ozone to date are not supported by observations, suggesting that significant uncertainties remain. • Midlatitude total column ozone is simulated to evolve differently in the two hemispheres. Over northern midlatitudes, annually averaged total column ozone is projected to return to 1980 values between 2015 and 2030, while for southern midlatitudes the return to 1980 values is projected to occur between 2030 and 2040. The more rapid return to 1980 values in northern midlatitudes is linked to a more pronounced strengthening of the poleward transport of ozone due to the effects of increased GHG levels, and effects of Antarctic ozone depletion on southern midlatitudes. By 2100, midlatitude total column ozone is projected to be above 1980 values in both hemispheres. • October-mean Antarctic total column ozone is projected to return to 1980 levels after midcentury, later than in any other region, and yet earlier than when stratospheric halogen loading is projected to return to 1980 levels. The slightly earlier return of ozone to 1980 levels (2045–2060) results primarily from upper stratospheric cooling and resultant increases in ozone. The return of polar halogen loading to 1980 levels (2050–2070) in CCMs is earlier than in empirical models that exclude the effects of GHG-induced changes in circulation. Our confidence in the drivers of changes in Antarctic ozone is higher than for other regions because (i) ODSs exert a strong influence on Antarctic ozone, (ii) the effects of changes in GHG abundances are comparatively small, and (iii) projections of ODS emissions are more certain than those for GHGs. Small Antarctic ozone holes (areas of ozone <220 Dobson units, DU) could persist to the end of the 21st century. • March-mean Arctic total column ozone is projected to return to 1980 levels two to three decades before polar halogen loading returns to 1980 levels, and to exceed 1980 levels thereafter. While CCM simulations project a return to 1980 levels between 2020 and 2035, most models tend not to capture observed low temperatures and thus underestimate present-day Arctic ozone loss such that it is possible that this return date is biased early. Since the strengthening of the Brewer-Dobson circulation through the 21st century leads to increases in springtime Arctic column ozone, by 2100 Arctic ozone is projected to lie well above 1960 levels. Uncertainties in Projections • Conclusions dependent on future GHG levels are less certain than those dependent on future ODS levels since ODS emissions are controlled by the Montreal Protocol. For the six GHG scenarios considered by a few CCMs, the simulated differences in stratospheric column ozone over the second half of the 21st century are largest in the northern midlatitudes and the Arctic, with maximum differences of 20–40 DU between the six scenarios in 2100. • There remain sources of uncertainty in the CCM simulations. These include the use of prescribed ODS mixing ratios instead of emission fluxes as lower boundary conditions, the range of sea surface temperatures and sea ice concentrations, missing tropospheric chemistry, model parameterizations, and model climate sensitivity. • Geoengineering schemes for mitigating climate change by continuous injections of sulfur-containing compounds into the stratosphere, if implemented, would substantially affect stratospheric ozone, particularly in polar regions. Ozone losses observed following large volcanic eruptions support this prediction. However, sporadic volcanic eruptions provide limited analogs to the effects of continuous sulfur emissions. Preliminary model simulations reveal large uncertainties in assessing the effects of continuous sulfur injections. Expected Future Changes in Surface UV. While a number of factors, in addition to ozone, affect surface UV irradiance, the focus in this chapter is on the effects of changes in stratospheric ozone on surface UV. For this reason, clear-sky surface UV irradiance is calculated from ozone projections from CCMs. • Projected increases in midlatitude ozone abundances during the 21st century, in the absence of changes in other factors, in particular clouds, tropospheric aerosols, and air pollutants, will result in decreases in surface UV irradiance. Clear-sky erythemal irradiance is projected to return to 1980 levels on average in 2025 for the northern midlatitudes, and in 2035 for the southern midlatitudes, and to fall well below 1980 values by the second half of the century. However, actual changes in surface UV will be affected by a number of factors other than ozone. • In the absence of changes in other factors, changes in tropical surface UV will be small because changes in tropical total column ozone are projected to be small. By the middle of the 21st century, the model projections suggest surface UV to be slightly higher than in the 1960s, very close to values in 1980, and slightly lower than in 2000. The projected decrease in tropical total column ozone through the latter half of the century will likely result in clear-sky surface UV remaining above 1960 levels. Average UV irradiance is already high in the tropics due to naturally occurring low total ozone columns and high solar elevations. • The magnitude of UV changes in the polar regions is larger than elsewhere because ozone changes in polar regions are larger. For the next decades, surface clear-sky UV irradiance, particularly in the Antarctic, will continue to be higher than in 1980. Future increases in ozone and decreases in clear-sky UV will occur at slower rates than those associated with the ozone decreases and UV increases that occurred before 2000. In Antarctica, surface clear-sky UV is projected to return to 1980 levels between 2040 and 2060, while in the Arctic this is projected to occur between 2020 and 2030. By 2100, October surface clear-sky erythemal irradiance in Antarctica is likely to be between 5% below to 25% above 1960 levels, with considerable uncertainty. This is consistent with multi-model-mean October Antarctic total column ozone not returning to 1960 levels by 2100. In contrast, by 2100, surface clear-sky UV in the Arctic is projected to be 0–10% below 1960 levels.

Enhanced sensitivity to rapamycin following long-term oestrogen deprivation in MCF-7, T-47-D and ZR-75-1 human breast cancer cells

Human breast cancer cells (MCF-7, T-47-D and ZR-75-1) can adapt to circumvent any reduced growth rate during long-term oestrogen deprivation, and this provides three model systems to investigate mechanisms of endocrine resistance in breast cancer. In this paper we report consistent differences in the effects of three growth inhibitors following long-term oestrogen deprivation in all three cell models. Long-term oestrogen deprivation of MCF-7, T-47-D and ZR-75-1 cells resulted in reduced growth inhibition by PD98059 (2–10 µg/ml), implying a loss of dependence on mitogen-activated protein kinase pathways for growth. The growth inhibitor LY294002 (2–10 µM) inhibited growth of both oestrogen-maintained and oestrogen-deprived cells with similar dose–responses, implying continued similar dependence on phosphoinositide 3-kinase (PI3K) pathways with no alteration after adaptation to oestrogen independent growth. However, by contrast, long-term oestrogen deprivation resulted in an increased sensitivity to growth inhibition by rapamycin, which was not reduced by readdition of oestradiol. The enhanced inhibition of long-term oestrogen-deprived MCF-7-ED, T-47-D-ED and ZR-75-1-ED cell growth by combining rapamycin with LY294002 at concentrations where each alone had little effect, offers preclinical support to the development of therapeutic combinations of rapamycin analogues with other PI3K inhibitors in endocrine-resistant breast cancer.

Algorithmic statistical analysis of electrophysiological data for the investigation of structure-activity relationship in single neurons

We are developing computational tools supporting the detailed analysis of the dependence of neural electrophysiological response on dendritic morphology. We approach this problem by combining simulations of faithful models of neurons (experimental real life morphological data with known models of channel kinetics) with algorithmic extraction of morphological and physiological parameters and statistical analysis. In this paper, we present the novel method for an automatic recognition of spike trains in voltage traces, which eliminates the need for human intervention. This enables classification of waveforms with consistent criteria across all the analyzed traces and so it amounts to reduction of the noise in the data. This method allows for an automatic extraction of relevant physiological parameters necessary for further statistical analysis. In order to illustrate the usefulness of this procedure to analyze voltage traces, we characterized the influence of the somatic current injection level on several electrophysiological parameters in a set of modeled neurons. This application suggests that such an algorithmic processing of physiological data extracts parameters in a suitable form for further investigation of structure-activity relationship in single neurons.

Linear-wavelet models for non-linear identification applied to a pressure plant

A nonlinear regression structure comprising a wavelet network and a linear term is proposed for system identification. The theoretical foundation of the approach is laid by proving that radial wavelets are orthogonal to linear functions. A constructive procedure for building such models is described and the approach is tested with experimental data.

Linear-wavelet models for system identification

A model structure comprising a wavelet network and a linear term is proposed for nonlinear system identification. It is shown that under certain conditions wavelets are orthogonal to linear functions and, as a result, the two parts of the model can be identified separately. The linear-wavelet model is compared to a standard wavelet network using data from a simulated fermentation process. The results show that the linear-wavelet model yields a smaller modelling error when compared to a wavelet network using the same number of regressors.

Structure variation and evolution in microphase-separated grafted diblock copolymer films

The phase behavior of grafted d-polystyrene-block-poly(methyl methacrylate) diblock copolymer films is examined, with particular focus on the effect of solvent and annealing time. It was observed that the films undergo a two-step transformation from an initially disordered state, through an ordered metastable state, to the final equilibrium configuration. It was also found that altering the solvent used to wash the films, or complete removal of the solvent prior to thermal annealing using supercritical CO2, could influence the structure of the films in the metastable state, though the final equilibrium state was unaffected. To aid in the understanding to these experimental results, a series of self-consistent field theory calculations were done on a model diblock copolymer brush containing solvent. Of the different models examined, those which contained a solvent selective for the grafted polymer block most accurately matched the observed experimental behavior. We hypothesize that the structure of the films in the metastable state results from solvent enrichment of the film near the film/substrate interface in the case of films washed with solvent or faster relaxation of the nongrafted block for supercritical CO2 treated (solvent free) films. The persistence of the metastable structures was attributed to the slow reorganization of the polymer chains in the absence of solvent.

The effects of landscape modifications on the long-term persistence of animal populations

Background: The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Methodology/Principal Findings: Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Significance: Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.