Variable selection in high-dimensional data: application in a SARS-CoV-2 pneumonia clinical data-set

As a result of the COVID-19 pandemic that collapsed hospitals in some countries, numerous studies have been carried out to understand the development of the disease and how it affects patients with different characteristics, in order to make optimal use of the available resources. This project is part of a multicentre study that aims to predict the severity of patients with SARS-CoV-2 pneumonia, for which different variables related to health, demographic and socio-economic factors and exposure to pollutants of patients have been collected. Given the number of variables contained in the data-set, it is necessary to reduce the number of variables in order to create a practical model for interpretation, as well as to reduce the amount of information that doctors have to collect on each patient. In this project, an exhaustive analysis of variable or feature selection techniques has been carried out in order to determine their performance and relevance in terms of stability, similarity and computation time. Based on the techniques that have shown the best characteristics, the most meaningful factors in preventing the severity of pneumonia have been identified, in accordance with what has been proposed by other studies

Chapter 6 • Hybrid seismic imaging

In the geophysics of oil exploration and reservoir studies, the surface seismic method is the most commonly used method to obtain a subsurface model in 2 or 3 dimensions. This method plays an increasingly important role in soil investigations for geotechnical, hydrogeological and site characterization studies regarding seismic hazard issues. The goal of this book is to provide a practical guide, using examples from the field, to the application of seismic methods to surface imaging. After reviewing the current state of knowledge in seismic wave propagation, refraction and reflection seismic methods, the book aims to describe how seismic tomography and fullwave form inversion methods can be used to obtain seismic images of the subsurface. Through various synthetic and field examples, the book highlights the benefit of combining different sets of data: refracted waves with reflected waves, and body waves with surface waves. With field data targeting shallow structures, it shows how more accurate geophysical models can be obtained by using the proposed hybrid methods. Finally, it shows how the integration of seismic data (3D survey and VSP), logging data (acoustic logging) and core measurements, combined with a succession of specific and advanced processing techniques, enables the development of a 3D high resolution geological model in depth. In addition to these examples, the authors provide readers with guidelines to carry out these operations, in terms of acquisition, as well as processing and interpretation. In each chapter, the reader will find theoretical concepts, practical rules and, above all, actual application examples. For this reason, the book can be used as a text to accompany course lectures or continuing education seminars. This book aims to promote the exchange of information among geologists, geophysicists, and engineers in geotechnical fields

Degradation of Anthracycline Antitumor Compounds Catalysed by Metal Ions

The influence of some metal ions on the degradation of anthracyclines was examined. One of the degradation products is the 7,8-dehydro-9,10-desacetyldoxorubicinone, D* (¥), usually formed by hydrolysis at slightly basic pH. D* is a lipophilic compound with no cytostatic properties. Its formation could be responsible for the lack of antitumor activity of the parent compound. The coordination of metal ions to anthracycline derivatives is required to have degradation products. Cations such as Na+, K+, or Ca2+ do not induce the D* formation however metals which can form stable complexes with doxorubicin afford D*. Iron(III) and copper(II) form appreciable amount of D* at slightly acidic pH. Terbium(III) forms D* but its complex is stable only at slightly basic pH. Palladium(II) which does not form D*. The influence of the coordination mode of metal ions to anthracycline on the D* formation is discussed

Cambios en la composición de esteroles del aceite de cardo mariano (Silybium marianum L.) durante la maduración de la semilla

In this study, the total lipid content and sterol compositions were determined during the development of milk thistle seeds. The oil content increased to a maximum value of 36±1.7% and then declined to reach a value of 30.5±0.9% at full maturity. The sterol content of milk thistle seeds was affected by the ripening degree of the seeds. At the early stages of seed maturation, Δ7-stigmastenol was the most abundant sterol followed by β-sitosterol. However, at full maturity, β-sitosterol was the most predominant sterol (46.50±0.8%). As the seed developed, campesterol and stigmasterol amounts increased, while Δ7-avenasterol content decreased. It can be concluded that milk thistle seed oil has a characteristic sterol pattern comparable to the ones elucidated for olive oil and corn oil. The extracted oil from milk thistle seeds is rich in phytosterols and could be used in food preparation and human nutrition.En este estudio se determinaron la composición de lípidos totales y esteroles durante el desarrollo de semillas de cardo mariano. El contenido de aceite incrementó a un valor máximo de 36±1,7% y posteriormente disminuyó hasta alcanzar un valor de 30,5±0,9% cuando la maduración fue completa. El contenido de esteroles de las semillas de cardo mariano se ve afectado por el grado de maduración de las semillas. En las primeras etapas de la maduración de las semillas el Δ7-estigmastenol fué el esterol más abundante, seguido de β-sitosterol. Sin embargo en plena madurez, β-sitosterol fue el esterol predominante (46,50±0,8%). A medida que las semillas se desarrollan las cantidades de campesterol y estigmasterol aumentan, mientras que el contenido Δ7-avenasterol disminuye. Se puede concluir que el aceite de semillas de cardo mariano tiene un patrón característico de esteroles en comparación con lo especificado para los aceites de oliva y de maíz. El aceite extraído de las semillas del cardo mariano es rica en fitoesteroles y podría ser utilizado en la preparación de alimentos y en nutrición humana

In vitro feeding of all life stages of two-host Hyalomma excavatum and Hyalomma scupense and three-host Hyalomma dromedarii ticks

Ticks are blood-sucking ectoparasites and can transmit various pathogens of medical and veterinary relevance. The life cycle of ticks can be completed under laboratory conditions on experimental animals, but the artificial feeding of ticks has attracted increased interest as an alternative method. This study represents the first report on the successful in vitro feeding of all life stages of two-host tick species, Hyalomma scupense and Hyalomma excavatum, and the three-host tick Hyalomma dromedarii. The attachment and engorgement rates of adults were 84% (21/25) and 76% (19/25) for H. scupense females. For adult H. excavatum and H. dromedarii, 70% (21/30) and 34.4% (11/32) of the females attached and all attached females successfully fed to repletion. The oviposition rates of the artificially fed females were 36.4%, 57.1% and 63.1% for H. dromedarii, H. excavatum and H. scupense, respectively, with a reproductive efficiency index varying between 44.3 and 60.7%. For the larvae, the attachment and engorgement rates were 44.2% (313/708) and 42.8% (303/708) for H. dromedarii, 70.5% (129/183) and 56.8% (104/183) for H. excavatum and 92.6% (113/122) and 55.7% (68/122) for H. scupense. The attachment and engorgement rates for the nymphs were 90.2% (129/143) and 47.6% (68/143) for H. dromedarii, 66.7% (34/51) and 41.2% (21/51) for H. excavatum, and 44.1% (30/68) and 36.8% (25/68) for H. scupense. Molting rates of the immature stages varied between 71.3% (216/303) and 100% (68/68) for the larvae and between 61.9% (13/21) and 96% (24/25) for the nymphs. The successful in vitro feeding of all stages of the three Hyalomma species makes this method a valuable tool for tick research, with potential applications in studies on the pathogens transmitted by these tick species such as Theileria annulata

Extracting relevant predictive variables for COVID-19 severity prognosis: An exhaustive comparison of feature selection techniques

With the COVID-19 pandemic having caused unprecedented numbers of infections and deaths, large research efforts have been undertaken to increase our understanding of the disease and the factors which determine diverse clinical evolutions. Here we focused on a fully data-driven exploration regarding which factors (clinical or otherwise) were most informative for SARS-CoV-2 pneumonia severity prediction via machine learning (ML). In particular, feature selection techniques (FS), designed to reduce the dimensionality of data, allowed us to characterize which of our variables were the most useful for ML prognosis. We conducted a multi-centre clinical study, enrolling n=1548 patients hospitalized due to SARS-CoV-2 pneumonia: where 792, 238, and 598 patients experienced low, medium and high-severity evolutions, respectively. Up to 106 patient-specific clinical variables were collected at admission, although 14 of them had to be discarded for containing ⩾60% missing values. Alongside 7 socioeconomic attributes and 32 exposures to air pollution (chronic and acute), these became d=148 features after variable encoding. We addressed this ordinal classification problem both as a ML classification and regression task. Two imputation techniques for missing data were explored, along with a total of 166 unique FS algorithm configurations: 46 filters, 100 wrappers and 20 embeddeds. Of these, 21 setups achieved satisfactory bootstrap stability (⩾0.70) with reasonable computation times: 16 filters, 2 wrappers, and 3 embeddeds. The subsets of features selected by each technique showed modest Jaccard similarities across them. However, they consistently pointed out the importance of certain explanatory variables. Namely: patient’s C-reactive protein (CRP), pneumonia severity index (PSI), respiratory rate (RR) and oxygen levels –saturation SpO2, quotients SpO2/RR and arterial SatO2/FiO2 –, the neutrophil-to-lymphocyte ratio (NLR) –to certain extent, also neutrophil and lymphocyte counts separately–, lactate dehydrogenase (LDH), and procalcitonin (PCT) levels in blood. A remarkable agreement has been found a posteriori between our strategy and independent clinical research works investigating risk factors for COVID-19 severity. Hence, these findings stress the suitability of this type of fully data-driven approaches for knowledge extraction, as a complementary to clinical perspectives

Imaging and pathology findings after an initial negative MRI-US fusion-guided and 12-core extended sextant prostate biopsy session

PURPOSEA magnetic resonance imaging-ultrasonography (MRI-US) fusion-guided prostate biopsy increases detection rates compared to an extended sextant biopsy. The imaging characteristics and pathology outcomes of subsequent biopsies in patients with initially negative MRI-US fusion biopsies are described in this study.MATERIALS AND METHODSWe reviewed 855 biopsy sessions of 751 patients (June 2007 to March 2013). The fusion biopsy consisted of two cores per lesion identified on multiparametric MRI (mpMRI) and a 12-core extended sextant transrectal US (TRUS) biopsy. Inclusion criteria were at least two fusion biopsy sessions, with a negative first biopsy and mpMRI before each.RESULTSThe detection rate on the initial fusion biopsy was 55.3%; 336 patients had negative findings. Forty-one patients had follow-up fusion biopsies, but only 34 of these were preceded by a repeat mpMRI. The median interval between biopsies was 15 months. Fourteen patients (41%) were positive for cancer on the repeat MRI-US fusion biopsy. Age, prostate-specific antigen (PSA), prostate volume, PSA density, digital rectal exam findings, lesion diameter, and changes on imaging were comparable between patients with negative and positive rebiopsies. Of the patients with positive rebiopsies, 79% had a positive TRUS biopsy before referral (P = 0.004). Ten patients had Gleason 3+3 disease, three had 3+4 disease, and one had 4+4 disease.CONCLUSIONIn patients with a negative MRI-US fusion prostate biopsy and indications for repeat biopsy, the detection rate of the follow-up sessions was lower than the initial detection rate. Of the prostate cancers subsequently found, 93% were low grade (≤3+4). In this low risk group of patients, increasing the follow-up time interval should be considered in the appropriate clinical setting

Imaging Geological Structures Up to the Acquisition Surface Using a Hybrid Refraction-Reflection Seismic Method

The aim of seismic imaging is to reconstruct the reflectivity associated with subsurface structures. In standard imaging techniques, the reflectivity model usually starts a few meters below the surface, the actual depth being dependent on data acquisition parameters and the mute used to remove stretching of first arrivals after normal moveout correction. In this paper, we describe a method to image the reflectivity of near-surface structures starting from the acquisition surface. This is achieved by processing both the first arrivals and the reflected phases present in data collected for refraction surveys. The proposed imaging procedure works in three steps. First, we obtain a velocity model for the shallow region by combining the Plus-Minus method of refraction interpretation with tomographic inversion of first arrival times. Second, by processing reflection events present in the refraction data, we obtain a standard reflectivity section for the deeper region. Finally, we compute reflectivity for the shallow region using the velocity model estimated from first arrival information in step 1. This velocity model is used both to compute reflectivity and to convert it in time. The reflectivity obtained for the shallow region is associated with velocity contrasts. In order to merge it with the reflectivity section for the deeper region a scaling factor between the two sets of reflectivity sections must be computed and applied. The novelty of this contribution is the use the tomographic velocity model in evaluating reflectivity for the upper part of the section. This improves the continuity of information about all near-surface structures in comparison with previous works that were limited to reflection data. Three field examples illustrate the proposed procedure showing continuous information about reflectivity of structures starting from the acquisition surface