Estimation of Relevant Variables on High-Dimensional Biological Patterns Using Iterated Weighted Kernel Functions

BACKGROUND The analysis of complex proteomic and genomic profiles involves the identification of significant markers within a set of hundreds or even thousands of variables that represent a high-dimensional problem space. The occurrence of noise, redundancy or combinatorial interactions in the profile makes the selection of relevant variables harder. METHODOLOGY/PRINCIPAL FINDINGS Here we propose a method to select variables based on estimated relevance to hidden patterns. Our method combines a weighted-kernel discriminant with an iterative stochastic probability estimation algorithm to discover the relevance distribution over the set of variables. We verified the ability of our method to select predefined relevant variables in synthetic proteome-like data and then assessed its performance on biological high-dimensional problems. Experiments were run on serum proteomic datasets of infectious diseases. The resulting variable subsets achieved classification accuracies of 99% on Human African Trypanosomiasis, 91% on Tuberculosis, and 91% on Malaria serum proteomic profiles with fewer than 20% of variables selected. Our method scaled-up to dimensionalities of much higher orders of magnitude as shown with gene expression microarray datasets in which we obtained classification accuracies close to 90% with fewer than 1% of the total number of variables. CONCLUSIONS Our method consistently found relevant variables attaining high classification accuracies across synthetic and biological datasets. Notably, it yielded very compact subsets compared to the original number of variables, which should simplify downstream biological experimentation

A cost-effective algae-based biosensor for water quality analysis: Development and testing in collaboration with peasant communities

New anthropic potentially harmful compounds are released into the environment everyday. In this context, broad range bioassays have emerged providing economically viable and widely applicable alternatives due to their ability to detect the cumulative toxicity of mixtures of both known and unknown chemicals in a sample, thus allowing direct information about water quality. Here we present a low-cost, wide-range algae-based biosensor that is easy to assemble and operate by untrained users and provides direct readings. It was developed as a request of a peasant social movement organization to assess the toxicity of drinking water in rural communities affected by pesticide spraying. Two fresh water algae strains, Scenedesmus acutus and Pseudokirchneriella subcapitata, were immobilized in alginate beads and tested as bioindicators. After incubation with different pollutants for five days, naked eye analysis by several observers proved to be a successful method to survey algae’s growth and establish the detection limits. Best detection limits were 10 ppm for technical-grade acid glyphosate, 15 ppm for glyphosate-based formulation, 50 ppb for atrazine formulation, 7.5 ppm for copper and 250 ppb for chromium. Absorbance measurements upon algae resuspension validated these results. The developed device was successfully tested in participatory workshops conducted at rural communities. Children, adults and elders with no scientific training were able to build the sensor and interpret the results, thus evaluating the quality of rain and well water used in their communities.Universidad Nacional de Santiago del EsteroConsejo Nacional de Investigaciones Científicas y Técnica

Traditional knowledge and cultural importance of Borassus aethiopum Mart. in Benin: interacting effects of socio-demographic attributes and multi-scale abundance

ResearchBackground: Eliciting factors affecting distribution of traditional knowledge (TK) and cultural importance of plant resources is central in ethnobiology. Socio-demographic attributes and ecological apparency hypothesis (EAH) have been widely documented as drivers of TK distribution, but their synergistic effect is poorly documented. Here, we focused on Borassus aethiopum, a socio-economic important agroforestry palm in Africa, analyzing relationships between the number of use-reports and cultural importance on one hand, and informant socio-demographic attributes (age category and gender) on the other hand, considering the EAH at multi-scale contexts. Our hypothesis is that effects of socio-demographic attributes on use-reports and cultural importance are shaped by both local (village level) and regional (chorological region level) apparency of study species. We expected so because distribution of knowledge on a resource in a community correlates to the versatility in the resource utilization but also connections among communities within a region. Methods: Nine hundred ninety-two face-to-face individual semi-structured interviews were conducted in six villages of low versus high local abundance of B. aethiopum spanning three chorological regions (humid, sub-humid and semiarid) also underlying a gradient of increasing distribution and abundance of B. aethiopum. Number of use-reports and score of importance of uses of B. aethiopum were recorded in six use-categories including medicine, food, handcraft, construction, firewood, and ceremonies and rituals. Data were analyzed using Poisson and ordered logistic modelsinfo:eu-repo/semantics/publishedVersio

Resistindo ao desenvolvimento neocolonial: a luta do povo de Andalgalá contra projetos megamineiros

A América Latina vem experimentando uma nova era de declarada fé dos governos no mito do desenvolvimento, em articulação com a expansão de políticas extrativistas exportadoras em um contexto de renovada dependência. A face mais dramática do extrativismo na região tem sido a crescente presença de corporações mineiras transnacionais apoiadas por governos nacionais e regionais e por instituições internacionais financeiras e de apoio ao desenvolvimento, e intensamente resistidas por movimentos sociais populares. Neste artigo apresentamos o caso de Andalgalá (uma pequena cidade na Província de Catamarca, na Argentina) e as lutas do povo contra corporações mineiras transnacionais e seus aliados. Na tradição da Filosofia da Libertação e do método ana-dialético de Dussel, nos engajamos com o que tem sido denominado "comunidades argentinas do NÃO", expressando sua oposição a formas neocoloniais de desenvolvimento e gestão. Neste artigo estamos especificamente interessados em compreender como dois dispositivos gerencialistas usados pelas corporações mineiras, responsabilidade social corporativa (RSC) e pactos de governança, impactam a luta do povo. Acima de tudo, este artigo oferece instantâneos de batalhas na linha de frente do extrativismo. Esperamos ter dado voz àquelas pessoas que normalmente não são ouvidas, criando um espaço para suas visões sobre um tipo diferente de desenvolvimento.</jats:p

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Role of miR-2392 in driving SARS-CoV-2 infection

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provide an exciting avenue toward antiviral therapeutics. From patient transcriptomic data, we determined that a circulating miRNA, miR-2392, is directly involved with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia, as well as promoting many symptoms associated with coronavirus disease 2019 (COVID-19) infection. We demonstrate that miR-2392 is present in the blood and urine of patients positive for COVID-19 but is not present in patients negative for COVID-19. These findings indicate the potential for developing a minimally invasive COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we design a miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters, and may potentially inhibit a COVID-19 disease state in humans

Pollination networks along the sea-inland gradient reveal landscape patterns of keystone plant species

Linking the functional role of plants and pollinators in pollination networks to ecosystem functioning and resistance to perturbations can represent a valuable knowledge to implement sound conservation and monitoring programs. The aim of this study was to assess the resistance of pollination networks in coastal dune systems and to test whether pollination interactions have an explicit spatial configuration and whether this affect network resistance. To this aim, we placed six permanent 10 m-wide belt transects. Within each transect we placed five plots of 2 m x 2 m, in order to catch the different plant communities along the dune sequence. We monitored pollination interactions between plants and pollinators every 15 days during the overall flowering season. The resulting networks of pollination interactions showed a relatively low degree of resistance. However, they had a clear spatial configuration, with plant species differently contributing to the resistance of pollination networks occurring non-randomly from the seashore inland. Our results evidenced that beside contributing to the creation and maintenance of dune ridges, thereby protecting inland communities from environmental disturbance, plant species of drift line and shifting dune communities have also a crucial function in conferring resistance to coastal dune pollination networks