Javier Palarea-Albaladejo

Universitat de Girona | UDG · Department of Computer Science and Applied Mathematics

Background Chlamydia abortus is one of the most diagnosed causes of infectious abortion in small ruminants. Infections can be controlled using the live, attenuated C. abortus strain 1B vaccine, which has been associated with infection and abortion in animals. This study aimed to compare the severity and the distribution of lesions caused by this va...

Phosphorus (P) pollution impairs river systems globally. There is long-standing interest in understanding catchment source P loads to inform mitigation to improve water quality. However, P sources to the hydrosphere differ individually in discharge behaviour, P intensity, bioavailability, and cumulative impacts. River condition also varies (e.g., r...

Composition of pyrolysis gases for wildland fuels is often determined using ground samples heated in non-oxidising environments. Results are applied to wildland fires where fuels change spatially and temporally, resulting in variable fire behaviour with variable heating. Though historically used, applicability of traditional pyrolysis results to th...

In this study, 18 animals were fed two forage-based diets: red clover (RC) and grass silage (GS), in a crossover-design experiment in which methane (CH 4 ) emissions were recorded in respiration chambers. Rumen samples obtained through naso-gastric sampling tubes were analysed by NMR. Methane yield (g/kg DM) was significantly lower from animals fed...

When aiming to assess the fat composition of commercial potato chip products, their diversity and the difficulties to verify the nutritional label of batches of chips by official methods are main challenges. Thus, the possibility of using alternative technologies is of great interest for both the industry and the public administration. Near-infrare...

Effective nutrient pollution mitigation measures require in-depth understanding of spatio- temporal controls on water quality which can be obtained by analyzing export regime and hysteresis patterns in concentration-discharge (c - Q) relationships. Such analyses require high-frequency data (hourly or higher resolution), hampering the assessment of...

Chlamydia abortus, the aetiological agent of enzootic abortion of ewes, is a major cause of reproductive loss in small ruminants worldwide, accounting for significant economic losses to the farming industry. Disease can be managed through the use of commercial inactivated or live whole organism-based vaccines, although both have limitations particu...

It often occurs in practice that it is sensible to give different weights to the variables involved in a multivariate data analysis—and the same holds for compositional data as multivariate observations carrying relative information. It can be convenient to apply weights to better accommodate differences in the quality of the measurements, the occu...

How we allocate time to activities impacts our health. Daily times spent in activities are interrelated because they compete for time-shares within a finite 24 h window. If more time is spent in one activity, time must be taken from one or more of the remaining activities to maintain the fixed total of 24 h. Thus, time-use data have a relative natu...

The time spent in different types of sleep, sedentary behaviour and physical activity during a day represents compositional data. Previous use of compositional analysis of daily activity data through orthonormal log-ratio coordinates in the form of pivot coordinates of four components (sleep, sedentary behaviour, light physical activity, moderate t...

Objective To examine the joint associations of daily time spent in different intensities of physical activity, sedentary behaviour and sleep with all-cause mortality. Methods Federated pooled analysis of six prospective cohorts with device-measured time spent in different intensities of physical activity, sedentary behaviour and sleep following a...

High‐throughput data representing large mixtures of chemical or biological signals are ordinarily produced in the molecular sciences. Given a number of samples, partial least squares (PLS) regression is a well‐established statistical method to investigate associations between them and any continuous response variables of interest. However, technica...

Chlamydia abortus infects livestock species worldwide and is the cause of enzootic abortion of ewes (EAE). In Europe, control of the disease is achieved using a live vaccine based on C. abortus 1B strain. Although the vaccine has been useful for controlling disease outbreaks, abortion events due to the vaccine have been reported. Recently, placenta...

Even though the logratio methodology provides a range of both generic, mostly exploratory, and purpose-built coordinate representations of compositional data, simple pairwise logratios are preferred by many for multivariate analysis in the geochemical practice, principally because of their simpler interpretation. However, the logratio coordinate sy...

We propose a robust procedure to estimate a linear regression model with compositional and real-valued explanatory variables. The proposed procedure is designed to be robust against individual outlying cells in the data matrix (cellwise outliers), as well as entire outlying observations (rowwise outliers). Cellwise outliers are first filtered and t...

Pyrolysate gas mixtures are multivariate and relative in nature. Statistical techniques applied to these data generally ignore their relative nature. Published data for permanent gases (CO, CO2, H2, CH4) and tars produced by pyrolysing 15 wildland fuels were reanalysed using compositional data analysis techniques. Mass and mole fractions were compo...

This book presents modern methods and real-world applications of compositional data analysis. It covers a wide variety of topics, ranging from an updated presentation of basic concepts and ideas in compositional data analysis to recent advances in the context of complex data structures. Further, it illustrates real-world applications in numerous sc...

Background: Physical activity levels are low in people with chronic obstructive pulmonary disease, and there is limited knowledge about how pulmonary rehabilitation transforms movement behaviors. This study analyzed data from a pulmonary rehabilitation trial and identified determinants of movement behaviors. Methods: Objectively assessed time in...

Genetic variation is associated with differences in disease resistance and susceptibility among individuals within a population. To date, molecular genetic analyses of host responses have relied on extraction of genomic DNA from whole blood or tissue samples. However, such samples are not routinely collected during large-scale field studies. We dem...

Ovine enzootic abortion (OEA) caused by the obligate intracellular bacterial pathogen Chlamydia abortus (C. abortus), is an endemic disease in most sheep-rearing countries worldwide. Following infection, C. abortus establishes a complex host-pathogen interaction with a latent phase in non-pregnant sheep followed by an active disease phase in the pl...

Chlamydia abortus is one of the most commonly diagnosed causes of infectious abortion in small ruminants worldwide. Control of the disease (Enzootic Abortion of Ewes or EAE) is achieved using the commercial live, attenuated C. abortus 1B vaccine strain, which can be distinguished from virulent wild-type (wt) strains by polymerase chain reaction-res...

A study was performed to examine any effect of hen age on the feeding ability and mortality of different life-stages of Dermanyssus gallinae [Poultry Red Mite (PRM)] when fed using a high welfare, on-hen mite feeding device. Mite feeding assays were carried out every two weeks on a cohort of five Lohman Brown hens with devices containing adult and...

Background: Researchers applying compositional data analysis to time-use data (e.g., time spent in physical behaviors) often face the problem of zeros, that is, recordings of zero time spent in any of the studied behaviors. Zeros hinder the application of compositional data analysis because the analysis is based on log-ratios. One way to overcome...

Soil mineral compositions are often complex and spatially diverse, with each mineral exhibiting characteristic chemical properties that determine the intrinsic total concentration of soil nutrients and their phyto-availability. Defining soil mineral-nutrient relationships is therefore important for understanding the inherent fertility of soils for...

The logratio-normal-multinomial distribution is a count data model resulting from compounding a multinomial distribution for the counts with a multivariate logratio-normal distribution for the multinomial event probabilities. However, the logratio-normal-multinomial probability mass function does not admit a closed form expression and, consequently...

Data describing the composition of smoke are inherently multivariate and always non-negative parts of a whole. The data are relative and the information is contained in the ratios between parts of the composition. A prior analysis of smoke emissions produced from the burning of manzanita wood mixed with low-density polyethylene plastic applied trad...

Food nutritional labeling is compulsory in the European Union since 13 December 2016. The analysis of all batches of foodstuff using the official methods is expensive and the food industry seeks cost-efficient solutions for measuring the components of nutritional labels. The information is commonly provided in the form of fractions or parts of a nu...

We aimed to compare all-cause mortality risk across clusters of adults 50+ (n = 1,035) with common lifestyle behaviors patterns in the National Health and Nutrition Examination Survey (2005-2006). Log-ratio coordinates of 24h movement pattern and z-scores of diet quality were used as input into a model-based clustering analysis. A Cox regression mo...

By conservation of mass, the mass of wildland fuel that is pyrolyzed and combusted must equal the mass of smoke emissions, residual char, and ash. For a given set of conditions, these amounts are fixed. This places a constraint on smoke emissions data that violates key assumptions for many of the statistical methods ordinarily used to analyze these...

This study presents the application of metabolomics to evaluate changes in the rumen metabolites of beef cattle fed with three different diet types: forage-rich, mixed and concentrate-rich. Rumen fluid samples were analysed by ¹H-NMR spectroscopy and the resulting spectra were used to characterise and compare metabolomic profiles between diet types...

In recent years, the focus of activity behavior research has shifted away from univariate paradigms (e.g., physical activity, sedentary behavior and sleep) to a 24-h time-use paradigm that integrates all daily activity behaviors. Behaviors are analyzed relative to each other, rather than as individual entities. Compositional data analysis (CoDA) is...

In functional data analysis some region(s) of the domain of the functions can be of more interest than others due to the quality of measurement, relative scale of the domain, or simply due to some external reason (e.g., interest of stakeholders). Weighting the domain is of interest particularly with probability density functions (PDFs), as derived...

Background: Evidence supporting the individual associations of sedentary behaviours with depression symptoms commonly ignores the inherent co-dependency between physical activity, sedentary behaviours and sleep in a given 24-hour period. Data analysis based on compositional methods effectively deals with this issue. Aim: To investigate the assoc...

Probability density functions (PDFs) can be understood as continuous compositions by the theory of Bayes spaces. The origin of a Bayes space is determined by a given reference measure. This can be easily changed through the well-known chain rule which has an impact on the geometry of the Bayes space. This work provides a mathematical framework for...

Specific Escherichia coli isolates lysogenised with prophages that express Shiga toxin (Stx) can be a threat to human health, with cattle being an important natural reservoir. In many countries the most severe pathology is associated with enterohaemorrhagic E. coli (EHEC) serogroups that express Stx subtype 2a. In the United Kingdom, phage type (PT...

The broken phosphorus (P) cycle has led to widespread eutrophication of freshwaters. Despite reductions in anthropogenic nutrient inputs that have led to improvement in the chemical status of running waters, corresponding improvements in their ecological status are often not observed. We tested a novel combination of complementary statistical model...

Foot-and-mouth disease (FMD) is a highly contagious viral infection of cloven hooved animals that continues to cause economic disruption in both endemic countries or when introduced into a formally FMD free country. Vaccines that protect against clinical disease and virus shedding are critical to control FMD. The replication deficient human adenovi...

Aims Previous prospective studies of the association between mortality and physical activity have generally not fully accounted for the interplay between movement behaviours. A compositional data modelling approach accounts for relative scale and co-dependency in time-use data across physical activity behaviours of the 24-hour day. Methods A prosp...

Survival analysis is commonly conducted in medical and public health research to assess the association of an exposure or intervention with a hard end outcome such as mortality. The Cox (proportional hazards) regression model is probably the most popular statistical tool used in this context. However, when the exposure includes compositional covari...

Water resources provide multiple services, one of the most important the provision of drinking water, conventionally treated before public consumption as potable supplies. With increasing pressures from land use and climate change, there are advantages to be gained from considering raw water quality as a fundamental characteristic of the natural re...

Objective: This study aimed to investigate the hypothesized negative association between duration of work time spent at a high relative aerobic workload and leisure time movement behaviours among blue-collar workers. Methods: This was a cross-sectional study based on heart rate and accelerometer data from 803 blue-collar workers (447 men and 356...

Minerals are the major component of most soils. Through direct inheritance from the parent material and subsequent alteration by chemical weathering, the soil mineral composition can be spatially diverse-reflecting the local geology, climate, and age of the soil. Each mineral present within the soil environment exhibits a characteristic chemical co...

Background Toxoplasma gondii is a zoonotic parasite of global importance. The outcome of infection in humans can depend on a number of factors including the infecting stage of the parasite, inoculating dose and virulence of the infecting strain. Molecular epidemiological studies have demonstrated an abundance of atypical strains of T. gondii in Sou...

Using data from five independent vaccine trials, which employed a subunit cocktail vaccine containing eight recombinant proteins to protect sheep against Teladorsagia circumcincta, a strategy was developed to simplify antigen complexity of the vaccine. A meta-analysis of data from these five trials demonstrated statistically significant reductions...

Mucosal antibody responses of sheep, at post-mortem, to the recombinant proteins used in Trial 6. Each data point represents the mean value (± S.E.M.) derived from nine sheep (eight-antigen group) or 10 sheep (all other groups). (A and B) Mean mucosal IgG and IgA levels, respectively, against wild-type T. circumcincta apyrase-1 (Tci-APY-1). (C and...

Antibody responses of sheep to the recombinant proteins used to immunise Group 1 (vaccinated sheep) in Trial 5. Each data point represents the mean value derived from 12 sheep. (A and B) Serum antibody responses for vaccinated sheep. (A) IgG; (B) IgA. (C and D) Abomasal mucosal antibody responses for vaccinated sheep at post-mortem. (C) IgG; (D) Ig...

Antibody responses of Group 2 (Control) sheep to the recombinant proteins used in Trial 5. Each data point represents the mean value derived from 12 sheep. (A and B) Serum antibody responses for control sheep. (A) IgG; (B) IgA. (C and D) Abomasal mucosal antibody responses (±S.E.M.) for these sheep at post-mortem. (C) IgG; (D) IgA.

Antibody responses of sheep to the recombinant proteins used in Trial 6. Each data point represents the mean value derived from nine sheep (A and B) or 10 sheep (C-F). (A and B) Serum antibody responses for sheep immunised with eight antigens. (A) IgG; (B) IgA. (C and D) Serum antibody responses for sheep in each group against wild type Tci-APY-1 (...

Optimisation and use of a device for the on-hen in vivo feeding of all hematophagous stages of Dermanyssus gallinae is described. The sealed mesh device contains the mites and is applied to the skin of the hen's thigh where mites can feed on the bird through a mesh which has apertures large enough to allow the mites’ mouth-parts to access to the bi...

Successful mammalian pregnancies are a result of complex physiological, endocrinological, and immunological processes that combine to create an environment where the mother is tolerant to the semi-allogeneic fetus. Our knowledge of the mechanisms that contribute to maternal tolerance is derived mainly from human and murine studies of haemochorial p...

This study investigates the association between the overall physical activity composition of the day (sedentary behavior (SB), light intensity physical activity (LIPA) and moderate-to-vigorous physical activity (MVPA)) and cardiometabolic health, and examines whether improved health can be associated with replacing SB with LIPA. A cross-sectional a...

Although there is an increasing awareness of the suitability of using compositional data methodology in public health research, classical methods of statistical analysis have been primarily used so far. The present study aims to illustrate the potential of robust statistics to model movement behaviour using Czech adolescent data. We investigated: (...

To develop effective sedentary behavior interventions aimed at people who are overweight/obese, detailed insight is needed into the contexts of sedentary behavior of these people. Therefore, the aims of this study were to describe the composition of sedentary behavior and to compare context-specific sedentary behaviors between different weight grou...

This study investigated the association between the allocation of time-use over the 24-h day between sleep, sedentary behaviour (SB), light-intensity physical activity (LPA) and moderate-to-vigorous-intensity physical activity (MVPA)) and health indicators. A cross-sectional analysis of Canadian Health Measures Survey data was undertaken using comp...

Leisure time physical activity (LTPA) is strongly associated with socioeconomic position (SEP). Few studies have investigated if demanding occupational physical activity (OPA) could impede a physically active lifestyle in low SEP groups. The aim of this study was to investigate the association between OPA and LTPA among low SEP men and women. We us...