Spatial surface-pattern analyses and boundary detection techniques applied in forest ecology

[EN] We review methods for uni- and multivariate surface pattern analysis and boundary detection used in forest ecology. A continuous surface pattern is defined as the locations of points (trees) in the space and the associated variable or variables. We illustrate useful methods to describe spatial patterns and infer the generating processes. We show the statistical basis and applied examples of univariate methods for binary (join counts) and quantitative variables (Moran and Geary correlograms, semivariograms, fractal dimension). We explain the calculus and interpretation of multivariate methods to describe surface patterns (Mantel test and correlogram) and their relationships with ordination methods. Finally, we show examples of techniques for boundary detection. Most analysed patterns corresponded to Pinus uncinata forests from the upper altitudinal limit in the Pyrenees or from a relict population. We discuss the advantages and disadvantages of each methodology and their applications in forest ecology.[ES] En este trabajo se revisan los métodos de análisis univariable y multivariable de los patrones de superficies y de detección de fronteras más utilizados en ecología forestal. El patrón de superficies es un patrón espacial continuo definido por las posiciones de los puntos (árboles) en el espacio y una o varias variables asociadas a cada punto. Se ilustran métodos útiles para describir patrones espaciales e inferir los procesos que los generaron. Se muestra el fundamento estadístico y ejemplos aplicados de métodos de análisis univariables para variables binarias (conteo contiguo) y cuantitativas (correlogramas de Moran y Geary, semivariogramas, dimensión fractal). Se detalla el cálculo e interpretación de métodos multivariables para la descripción de patrones de superficies (correlograma y test de Mantel) y su relación con los métodos de ordenación. Finalmente, se muestran ejemplos de métodos para la detección de fronteras. La mayor parte de los patrones reales analizados provienen de bosques de Pinus uncinata del límite altitudinal superior en los Pirineos o bien de una población relíctica. Se discuten las ventajas y desventajas de cada metodología y sus aplicaciones en ecología forestal.Los datos de Vinuesa se obtuvieron en el proyecto AMB95-0160 (CICyT).Peer reviewe

A comparative study of four intensive care outcome prediction models in cardiac surgery patients

<p>Abstract</p> <p>Background</p> <p>Outcome prediction scoring systems are increasingly used in intensive care medicine, but most were not developed for use in cardiac surgery patients. We compared the performance of four intensive care outcome prediction scoring systems (Acute Physiology and Chronic Health Evaluation II [APACHE II], Simplified Acute Physiology Score II [SAPS II], Sequential Organ Failure Assessment [SOFA], and Cardiac Surgery Score [CASUS]) in patients after open heart surgery.</p> <p>Methods</p> <p>We prospectively included all consecutive adult patients who underwent open heart surgery and were admitted to the intensive care unit (ICU) between January 1^st2007 and December 31^st2008. Scores were calculated daily from ICU admission until discharge. The outcome measure was ICU mortality. The performance of the four scores was assessed by calibration and discrimination statistics. Derived variables (Mean- and Max- scores) were also evaluated.</p> <p>Results</p> <p>During the study period, 2801 patients (29.6% female) were included. Mean age was 66.9 ± 10.7 years and the ICU mortality rate was 5.2%. Calibration tests for SOFA and CASUS were reliable throughout (p-value not < 0.05), but there were significant differences between predicted and observed outcome for SAPS II (days 1, 2, 3 and 5) and APACHE II (days 2 and 3). CASUS, and its mean- and maximum-derivatives, discriminated better between survivors and non-survivors than the other scores throughout the study (area under curve ≥ 0.90). In order of best discrimination, CASUS was followed by SOFA, then SAPS II, and finally APACHE II. SAPS II and APACHE II derivatives had discrimination results that were superior to those of the SOFA derivatives.</p> <p>Conclusions</p> <p>CASUS and SOFA are reliable ICU mortality risk stratification models for cardiac surgery patients. SAPS II and APACHE II did not perform well in terms of calibration and discrimination statistics.</p

Tactile Presentation of Network Data: Text, Matrix or Diagram?

Visualisations are commonly used to understand social, biological and other kinds of networks. Currently, we do not know how to effectively present network data to people who are blind or have low-vision (BLV). We ran a controlled study with 8 BLV participants comparing four tactile representations: organic node-link diagram, grid node-link diagram, adjacency matrix and braille list. We found that the node-link representations were preferred and more effective for path following and cluster identification while the matrix and list were better for adjacency tasks. This is broadly in line with findings for the corresponding visual representations.Comment: To appear in the ACM CHI Conference on Human Factors in Computing Systems (CHI 2020

High JC virus load in tongue carcinomas may be a risk factor for tongue tumorigenesis

The John Cunningham virus (JCV) asymptomatically infects a large proportion (~90%) of the population worldwide but may be activated in immunodeficient patients, resulting in progressive multifocal leukoencephalopathy. Recent reports demonstrated its oncogenic role in malignancies. In this paper, the presence of JCV-targeting T antigen was investigated in tongue carcinoma (TC, n = 39), dysplastic tongue epithelium (DTE, n = 15) and glossitis (n = 15) using real-time polymerase chain reaction (PCR) and in situ PCR and immunohistochemistry, and JCV copies were analyzed with the clinicopathological parameters of TCs. The results demonstrated that glossitis and DTEs had significantly lower copies of JCV (410.5 ± 44.3 and 658.3 ± 53.3 copies/μg DNA respectively) than TCs (981.5 ± 14.0, p  < 0.05). When they were divided into three groups with 0–200 copies/μg DNA (low), 201–1,000 (moderate) and more than 1001 (high), TCs showed 3 (7.6%) in the low group, 21 (53.8%) in the moderate group and 15 (38.4%) in the high group and glossitis showed 11 (73.3%) in the low group, 0 (0%) in the moderate group and 4 (26.6%) in the high group. The DTEs occupied an intermediate position between them (p < 0.001). In situ PCR demonstrated that the nuclei of TC and DTE cells are sporadically T-antigen positive but not in nasal turbinate epithelial cells. Immunohistochemistry for T-antigen protein revealed four positive cases only in TCs. The existence of JCV T-antigen DNA was not associated with the clinicopathological variables of TCs. In conclusion, the presence of JCV may be a risk factor of tongue carcinogenesis

Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures

The potassium-chloride co-transporter KCC2, encoded by SLC12A5, plays a fundamental role in fast synaptic inhibition by maintaining a hyperpolarizing gradient for chloride ions. KCC2 dysfunction has been implicated in human epilepsy, but to date, no monogenic KCC2-related epilepsy disorders have been described. Here we show recessive loss-of-function SLC12A5 mutations in patients with a severe infantile-onset pharmacoresistant epilepsy syndrome, epilepsy of infancy with migrating focal seizures (EIMFS). Decreased KCC2 surface expression, reduced protein glycosylation and impaired chloride extrusion contribute to loss of KCC2 activity, thereby impairing normal synaptic inhibition and promoting neuronal excitability in this early-onset epileptic encephalopathy

Functional Evolution of Duplicated Odorant-Binding Protein Genes, Obp57d and Obp57e, in Drosophila

Odorant-binding proteins (OBPs) are extracellular proteins found in insect chemosensilla, where they participate in the sensing of odors, tastes, and pheromones. Although a large number of OBP genes have been identified in insect genomes, their molecular functions and biological roles have been clarified in limited cases. Two OBP genes, Obp57d and Obp57e, were involved in the evolution of host-plant preference in Drosophila sechellia. Comparative analyses of the Obp57d/e genomic sequences from 27 closely related species suggested that the two genes arose by tandem gene duplication and functionally diverged from each other. In this study, the functional evolution of Obp57d and Obp57e was examined by in vitro binding assays using recombinant proteins synthesized in a bacterial system. Compared to the ancestral Dpse\OBP57de, Dmel\OBP57d was more specialized to tridecanoic acid while Dmel\OBP57e was generalized regarding their binding affinity, suggesting that the two OBP genes underwent subfunctionalization and neofunctionalization. A behavioral analysis using knockout flies supported that the biological role is different between OBP57d and OBP57e in vivo. Site-directed mutagenesis of the evolutionarily conserved amino acids revealed that these residues play an important role in protein folding. These findings provide a clue to understanding how the repertoire of OBP genes is maintained in a genome under natural selection