A cardiotoxicity dataset for breast cancer patients.

This dataset is a result of the collaboration between the University of A Coruña and the University Hospital of A Coruña. It contains information about 531 women diagnosed with HER2+ breast cancer, treated with potentially cardiotoxic oncologic therapies. These treatments can cause cardiovascular adverse events, including cardiac systolic dysfunction, the development of which has important clinical and prognostic implications. The availability of good predictors may enable early detection of these cardiac problems. Variables such as age, weight and height are available for each patient, as well as some measures obtained from echocardiography, a technique used prior and during the treatment to check the structure and function of the heart. Among them, there is a functional variable that measures the myocardial velocity during the cardiac cycle. For patients that experienced cancer therapy-related cardiac dysfunction during the treatment period, time until its appearance is known. This dataset aims to enable the scientific community in conducting new research on this cardiovascular side effect.

Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain.

Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at the community level. Here we describe COVIDBENS, a wastewater surveillance program running from June 2020 to March 2022 in the wastewater treatment plant of Bens in A Coruña (Spain). The main goal of this work was to provide an effective early warning tool based in wastewater epidemiology to help in decision-making at both the social and public health levels. RT-qPCR procedures and Illumina sequencing were used to weekly monitor the viral load and to detect SARS-CoV-2 mutations in wastewater, respectively. In addition, own statistical models were applied to estimate the real number of infected people and the frequency of each emerging variant circulating in the community, which considerable improved the surveillance strategy. Our analysis detected 6 viral load waves in A Coruña with concentrations between 103 and 106 SARS-CoV-2 RNA copies/L. Our system was able to anticipate community outbreaks during the pandemic with 8-36 days in advance with respect to clinical reports and, to detect the emergence of new SARS-CoV-2 variants in A Coruña such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529 and BA.2) in wastewater with 42, 30, and 27 days, respectively, before the health system did. Data generated here helped local authorities and health managers to give a faster and more efficient response to the pandemic situation, and also allowed important industrial companies to adapt their production to each situation. The wastewater-based epidemiology program developed in our metropolitan area of A Coruña (Spain) during the SARS-CoV-2 pandemic served as a powerful early warning system combining statistical models with mutations and viral load monitoring in wastewater over time.

Effectiveness of non-pharmaceutical interventions in nine fields of activity to decrease SARS-CoV-2 transmission (Spain, September 2020-May 2021).

Background: We estimated the association between the level of restriction in nine different fields of activity and SARS-CoV-2 transmissibility in Spain, from 15 September 2020 to 9 May 2021. Methods: A stringency index (0-1) was created for each Spanish province (n = 50) daily. A hierarchical multiplicative model was fitted. The median of coefficients across provinces (95% bootstrap confidence intervals) quantified the effect of increasing one standard deviation in the stringency index over the logarithmic return of the weekly percentage variation of the 7-days SARS-CoV-2 cumulative incidence, lagged 12 days. Results: Overall, increasing restrictions reduced SARS-CoV-2 transmission by 22% (RR = 0.78; one-sided 95%CI: 0, 0.82) in 1 week, with highest effects for culture and leisure 14% (0.86; 0, 0.98), social distancing 13% (0.87; 0, 0.95), indoor restaurants 10% (0.90; 0, 0.95) and indoor sports 6% (0.94; 0, 0.98). In a reduced model with seven fields, culture and leisure no longer had a significant effect while ceremonies decreased transmission by 5% (0.95; 0, 0.96). Models R 2 was around 70%. Conclusion: Increased restrictions decreased COVID-19 transmission. Limitations include remaining collinearity between fields, and somewhat artificial quantification of qualitative restrictions, so the exact attribution of the effect to specific areas must be done with caution.

Cure models to estimate time until hospitalization due to COVID-19: A case study in Galicia (NW Spain).

A short introduction to survival analysis and censored data is included in this paper. A thorough literature review in the field of cure models has been done. An overview on the most important and recent approaches on parametric, semiparametric and nonparametric mixture cure models is also included. The main nonparametric and semiparametric approaches were applied to a real time dataset of COVID-19 patients from the first weeks of the epidemic in Galicia (NW Spain). The aim is to model the elapsed time from diagnosis to hospital admission. The main conclusions, as well as the limitations of both the cure models and the dataset, are presented, illustrating the usefulness of cure models in this kind of studies, where the influence of age and sex on the time to hospital admission is shown.

Modeling the number of people infected with SARS-COV-2 from wastewater viral load in Northwest Spain.

The quantification of the SARS-CoV-2 RNA load in wastewater has emerged as a useful tool to monitor COVID-19 outbreaks in the community. This approach was implemented in the metropolitan area of A Coruña (NW Spain), where wastewater from a treatment plant was analyzed to track the epidemic dynamics in a population of 369,098 inhabitants. Viral load detected in the wastewater and the epidemiological data from A Coruña health system served as main sources for statistical models developing. Regression models described here allowed us to estimate the number of infected people (R2 = 0.9), including symptomatic and asymptomatic individuals. These models have helped to understand the real magnitude of the epidemic in a population at any given time and have been used as an effective early warning tool for predicting outbreaks in A Coruña municipality. The methodology of the present work could be used to develop a similar wastewater-based epidemiological model to track the evolution of the COVID-19 epidemic anywhere in the world where centralized water-based sanitation systems exist.

Estimating lengths-of-stay of hospitalised COVID-19 patients using a non-parametric model: a case study in Galicia (Spain).

Estimating the lengths-of-stay (LoS) of hospitalised COVID-19 patients is key for predicting the hospital beds' demand and planning mitigation strategies, as overwhelming the healthcare systems has critical consequences for disease mortality. However, accurately mapping the time-to-event of hospital outcomes, such as the LoS in the intensive care unit (ICU), requires understanding patient trajectories while adjusting for covariates and observation bias, such as incomplete data. Standard methods, such as the Kaplan-Meier estimator, require prior assumptions that are untenable given current knowledge. Using real-time surveillance data from the first weeks of the COVID-19 epidemic in Galicia (Spain), we aimed to model the time-to-event and event probabilities of patients' hospitalised, without parametric priors and adjusting for individual covariates. We applied a non-parametric mixture cure model and compared its performance in estimating hospital ward (HW)/ICU LoS to the performances of commonly used methods to estimate survival. We showed that the proposed model outperformed standard approaches, providing more accurate ICU and HW LoS estimates. Finally, we applied our model estimates to simulate COVID-19 hospital demand using a Monte Carlo algorithm. We provided evidence that adjusting for sex, generally overlooked in prediction models, together with age is key for accurately forecasting HW and ICU occupancy, as well as discharge or death outcomes.

Nonparametric covariate hypothesis tests for the cure rate in mixture cure models.

In lifetime data, like cancer studies, there may be long term survivors, which lead to heavy censoring at the end of the follow-up period. Since a standard survival model is not appropriate to handle these data, a cure model is needed. In the literature, covariate hypothesis tests for cure models are limited to parametric and semiparametric methods. We fill this important gap by proposing a nonparametric covariate hypothesis test for the probability of cure in mixture cure models. A bootstrap method is proposed to approximate the null distribution of the test statistic. The procedure can be applied to any type of covariate, and could be extended to the multivariate setting. Its efficiency is evaluated in a Monte Carlo simulation study. Finally, the method is applied to a colorectal cancer dataset.

Analysis of interval-grouped data in weed science: The binnednp Rcpp package.

Weed scientists are usually interested in the study of the distribution and density functions of the random variable that relates weed emergence with environmental indices like the hydrothermal time (HTT). However, in many situations, experimental data are presented in a grouped way and, therefore, the standard nonparametric kernel estimators cannot be computed.Kernel estimators for the density and distribution functions for interval-grouped data, as well as bootstrap confidence bands for these functions, have been proposed and implemented in the binnednp package. Analysis with different treatments can also be performed using a bootstrap approach and a Cramér-von Mises type distance. Several bandwidth selection procedures were also implemented. This package also allows to estimate different emergence indices that measure the shape of the data distribution. The values of these indices are useful for the selection of the soil depth at which HTT should be measured which, in turn, would maximize the predictive power of the proposed methods.This paper presents the functions of the package and provides an example using an emergence data set of Avena sterilis (wild oat).The binnednp package provides investigators with a unique set of tools allowing the weed science research community to analyze interval-grouped data.

ROC Curves for the Statistical Analysis of Microarray Data.

A receiver operating characteristic (ROC) curve is a graphical plot that illustrates the diagnostic ability of a binary classifier as a function of its discrimination threshold. This chapter is an overview on the use of ROC curves for microarray data. The notion of ROC curve and its motivation is introduced in Subheading 1. Relevant scientific contributions concerning the use of ROC curves for microarray data are briefly reviewed in Subheading 2. The special case with covariates is considered in Subheading 3. Two relevant aspects are reviewed in this section: the use of LASSO techniques for selecting and combining relevant markers and how to correct for multiple testing when a large number of markers are available. Finally, some conclusions are included.

Challenges and Future Trends for Microarray Analysis.

The current situation in microarray data analysis and prospects for the future are briefly discussed in this chapter, in which the competition between microarray technologies and high-throughput technologies is considered under a data analysis view. The up-to-date limitations of DNA microarrays are important to forecast challenges and future trends in microarray data analysis; these include data analysis techniques associated with an increasing sample sizes, new feature selection methods, deep learning techniques, covariate significance testing as well as false discovery rate methods, among other procedures for a better interpretability of the results.

Bootstrap testing for cross-correlation under low firing activity.

A new cross-correlation synchrony index for neural activity is proposed. The index is based on the integration of the kernel estimation of the cross-correlation function. It is used to test for the dynamic synchronization levels of spontaneous neural activity under two induced brain states: sleep-like and awake-like. Two bootstrap resampling plans are proposed to approximate the distribution of the test statistics. The results of the first bootstrap method indicate that it is useful to discern significant differences in the synchronization dynamics of brain states characterized by a neural activity with low firing rate. The second bootstrap method is useful to unveil subtle differences in the synchronization levels of the awake-like state, depending on the activation pathway.

Functional two-way analysis of variance and bootstrap methods for neural synchrony analysis.

BACKGROUND: Pairwise association between neurons is a key feature in understanding neural coding. Statistical neuroscience provides tools to estimate and assess these associations. In the mammalian brain, activating ascending pathways arise from neuronal nuclei located at the brainstem and at the basal forebrain that regulate the transition between sleep and awake neuronal firing modes in extensive regions of the cerebral cortex, including the primary visual cortex, where neurons are known to be selective for the orientation of a given stimulus. In this paper, the estimation of neural synchrony as a function of time is studied in data obtained from anesthetized cats. A functional data analysis of variance model is proposed. Bootstrap statistical tests are introduced in this context; they are useful tools for the study of differences in synchrony strength regarding 1) transition between different states (anesthesia and awake), and 2) affinity given by orientation selectivity. RESULTS: An analysis of variance model for functional data is proposed for neural synchrony curves, estimated with a cross-correlation based method. Dependence arising from the experimental setting needs to be accounted for. Bootstrap tests allow the identification of differences between experimental conditions (modes of activity) and between pairs of neurons formed by cells with different affinities given by their preferred orientations. In our test case, interactions between experimental conditions and preferred orientations are not statistically significant. CONCLUSIONS: The results reflect the effect of different experimental conditions, as well as the affinity regarding orientation selectivity in neural synchrony and, therefore, in neural coding. A cross-correlation based method is proposed that works well under low firing activity. Functional data statistical tools produce results that are useful in this context. Dependence is shown to be necessary to account for, and bootstrap tests are an appropriate method with which to do so.

Bursting thalamic responses in awake monkey contribute to visual detection and are modulated by corticofugal feedback.

The lateral geniculate nucleus is the gateway for visual information en route to the visual cortex. Neural activity is characterized by the existence of two firing modes: burst and tonic. Originally associated with sleep, bursts have now been postulated to be a part of the normal visual response, structured to increase the probability of cortical activation, able to act as a "wake-up" call to the cortex. We investigated a potential role for burst in the detection of novel stimuli by recording neuronal activity in the lateral geniculate nucleus (LGN) of behaving monkeys during a visual detection task. Our results show that bursts are often the neuron's first response, and are more numerous in the response to attended target stimuli than to unattended distractor stimuli. Bursts are indicators of the task novelty, as repetition decreased bursting. Because the primary visual cortex is the major modulatory input to the LGN, we compared the results obtained in control conditions with those observed when cortical activity was reduced by TMS. This cortical deactivation reduced visual response related bursting by 90%. These results highlight a novel role for the thalamus, able to code higher order image attributes as important as novelty early in the thalamo-cortical conversation.

Cross nearest-spike interval based method to measure synchrony dynamics.

A new synchrony index for neural activity is defined in this paper. The method is able to measure synchrony dynamics in low firing rate scenarios. It is based on the computation of the time intervals between nearest spikes of two given spike trains. Generalized additive models are proposed for the synchrony profiles obtained by this method. Two hypothesis tests are proposed to assess for differences in the level of synchronization in a real data example. Bootstrap methods are used to calibrate the distribution of the tests. Also, the expected synchrony due to chance is computed analytically and by simulation to assess for actual synchronization.

Influence of social support on older adults with cognitive impairment, depressive symptoms, or both coexisting.

The influence of social support dimensions (the extent of contact with others, the satisfaction with contacts, and the availability of help if sick or disabled) in elderly people with cognitive impairment (COG), depressive symptoms (DEP), or the co-occurrence of these symptoms (COG-DEP) was assessed in a cross-sectional analysis of a representative sample of 579 individuals aged 65 years and older. A lower extent of contact was related to COG (OR: 2.26). Fair satisfaction with contacts was related to DEP (OR: 2.88) and COG-DEP (OR: 4.22). A low level of satisfaction with contacts was an important predictor for DEP (OR: 7.99) and COG-DEP (OR: 7.88). Therefore, different dimensions of social support were independently correlated with different aspects of mental health. Quantitative aspects of social support were significantly linked to the presence of cognitive impairment. Satisfaction with social support affected depressive symptoms both alone and when they co-occurred with cognitive impairment.

Antagonist muscle co-activation during straight walking and its relation to kinematics: insight from young, elderly and Parkinson's disease.

Increased antagonist muscle co-activation of the lower limb during walking seems to be an adaptive process to the physiological changes of aging, in order to gain joint stability. In the healthy subjects this view seems to be reinforced by the fact that the co-activation index (CAI) increases when the gait is faster. The few reports on antagonist co-activation in Parkinson's disease (PD) patients indicate that they have larger co-activation than the healthy elderly, supporting the idea of the stabilization role of CAI during gait, as postural instability is a cardinal feature of PD. However it has also been reported that there is a reduction of the CAI when increasing velocity in PD or normal elderly. This questions the role of co-activation in stabilization during increased velocity. In this study we have analyzed the gait of healthy subjects (young and elderly), and PD patients (with and without freezing of gait, FOG) in order to better understand the relation between co-activation and gait kinematics, and to gain insight into the pathological changes associated with FOG in PD. We used Multiple Linear Regression models to study the relationship in shank muscles between CAI, velocity and cadence. Our results indicate that, for all groups of interest, the relationship between co-activation and the kinematics of gait is poor, due to the high degree of variability, questioning the explanatory value of the index.

Lasso logistic regression, GSoft and the cyclic coordinate descent algorithm: application to gene expression data.

Statistical methods generating sparse models are of great value in the gene expression field, where the number of covariates (genes) under study moves about the thousands while the sample sizes seldom reach a hundred of individuals. For phenotype classification, we propose different lasso logistic regression approaches with specific penalizations for each gene. These methods are based on a generalized soft-threshold (GSoft) estimator. We also show that a recent algorithm for convex optimization, namely, the cyclic coordinate descent (CCD) algorithm, provides with a way to solve the optimization problem significantly faster than with other competing methods. Viewing GSoft as an iterative thresholding procedure allows us to get the asymptotic properties of the resulting estimates in a straightforward manner. Results are obtained for simulated and real data. The leukemia and colon datasets are commonly used to evaluate new statistical approaches, so they come in useful to establish comparisons with similar methods. Furthermore, biological meaning is extracted from the leukemia results, and compared with previous studies. In summary, the approaches presented here give rise to sparse, interpretable models that are competitive with similar methods developed in the field.

A random effect multiplicative heteroscedastic model for bacterial growth.

BACKGROUND: Predictive microbiology develops mathematical models that can predict the growth rate of a microorganism population under a set of environmental conditions. Many primary growth models have been proposed. However, when primary models are applied to bacterial growth curves, the biological variability is reduced to a single curve defined by some kinetic parameters (lag time and growth rate), and sometimes the models give poor fits in some regions of the curve. The development of a prediction band (from a set of bacterial growth curves) using non-parametric and bootstrap methods permits to overcome that problem and include the biological variability of the microorganism into the modelling process. RESULTS: Absorbance data from Listeria monocytogenes cultured at 22, 26, 38, and 42 degrees C were selected under different environmental conditions of pH (4.5, 5.5, 6.5, and 7.4) and percentage of NaCl (2.5, 3.5, 4.5, and 5.5). Transformation of absorbance data to viable count data was carried out. A random effect multiplicative heteroscedastic model was considered to explain the dynamics of bacterial growth. The concept of a prediction band for microbial growth is proposed. The bootstrap method was used to obtain resamples from this model. An iterative procedure is proposed to overcome the computer intensive task of calculating simultaneous prediction intervals, along time, for bacterial growth. The bands were narrower below the inflection point (0-8 h at 22 degrees C, and 0-5.5 h at 42 degrees C), and wider to the right of it (from 9 h onwards at 22 degrees C, and from 7 h onwards at 42 degrees C). A wider band was observed at 42 degrees C than at 22 degrees C when the curves reach their upper asymptote. Similar bands have been obtained for 26 and 38 degrees C. CONCLUSIONS: The combination of nonparametric models and bootstrap techniques results in a good procedure to obtain reliable prediction bands in this context. Moreover, the new iterative algorithm proposed in this paper allows one to achieve exactly the prefixed coverage probability for the prediction band. The microbial growth bands reflect the influence of the different environmental conditions on the microorganism behaviour, helping in the interpretation of the biological meaning of the growth curves obtained experimentally.

Different sources of nitric oxide mediate neurovascular coupling in the lateral geniculate nucleus of the cat.

Understanding the link between neuronal responses (NRs) and metabolic signals is fundamental to our knowledge of brain function and it is a milestone in our efforts to interpret data from modern non invasive optical techniques such as fMRI, which are based on the close coupling between metabolic demand of active neurons and local changes in blood flow. The challenge is to unravel the link. Here we show, using spectrophotometry to record oxyhaemoglobin and methemoglobin (surrogate markers of cerebral flow and nitric oxide levels respectively) together with extracellular neuronal recordings in vivo and applying a multiple polynomial regression model, that the markers are able to predict up about 80% of variability in NR. Furthermore, we show that the coupling between blood flow and neuronal activity is heavily influenced by nitric oxide (NO). While NRs show the typical saturating response, blood flow shows a linear behaviour during contrast-response curves, with nitric oxide from different sources acting differently for low and high intensity.

Evaluating the ability of tree-based methods and logistic regression for the detection of SNP-SNP interaction.

Most common human diseases are likely to have complex etiologies. Methods of analysis that allow for the phenomenon of epistasis are of growing interest in the genetic dissection of complex diseases. By allowing for epistatic interactions between potential disease loci, we may succeed in identifying genetic variants that might otherwise have remained undetected. Here we aimed to analyze the ability of logistic regression (LR) and two tree-based supervised learning methods, classification and regression trees (CART) and random forest (RF), to detect epistasis. Multifactor-dimensionality reduction (MDR) was also used for comparison. Our approach involves first the simulation of datasets of autosomal biallelic unphased and unlinked single nucleotide polymorphisms (SNPs), each containing a two-loci interaction (causal SNPs) and 98 'noise' SNPs. We modelled interactions under different scenarios of sample size, missing data, minor allele frequencies (MAF) and several penetrance models: three involving both (indistinguishable) marginal effects and interaction, and two simulating pure interaction effects. In total, we have simulated 99 different scenarios. Although CART, RF, and LR yield similar results in terms of detection of true association, CART and RF perform better than LR with respect to classification error. MAF, penetrance model, and sample size are greater determining factors than percentage of missing data in the ability of the different techniques to detect true association. In pure interaction models, only RF detects association. In conclusion, tree-based methods and LR are important statistical tools for the detection of unknown interactions among true risk-associated SNPs with marginal effects and in the presence of a significant number of noise SNPs. In pure interaction models, RF performs reasonably well in the presence of large sample sizes and low percentages of missing data. However, when the study design is suboptimal (unfavourable to detect interaction in terms of e.g. sample size and MAF) there is a high chance of detecting false, spurious associations.