Modelling the optics of high resolution liquid crystal devices by the finite differences in the frequency domain method

A procedure combining accurate liquid crystal and electromagnetic modelling is developed for the analysis of wave propagation through liquid crystal devices. This is required to study the optics of high resolution liquid crystal cells or cells containing very small features, where diffraction effects occur. It is also necessary for the study of optical waveguiding devices using liquid crystal as variable permittivity substrates. An accurate finite element modelling program is used to find the permittivity tensor distribution, which is then used to find the response of the device to an excitation electromagnetic field by means of a finite difference in the frequency domain (FDFD) approach

On the performance of deep learning models for time series classification in streaming

Processing data streams arriving at high speed requires the development of models that can provide fast and accurate predictions. Although deep neural networks are the state-of-the-art for many machine learning tasks, their performance in real-time data streaming scenarios is a research area that has not yet been fully addressed. Nevertheless, there have been recent efforts to adapt complex deep learning models for streaming tasks by reducing their processing rate. The design of the asynchronous dual-pipeline deep learning framework allows to predict over incoming instances and update the model simultaneously using two separate layers. The aim of this work is to assess the performance of different types of deep architectures for data streaming classification using this framework. We evaluate models such as multi-layer perceptrons, recurrent, convolutional and temporal convolutional neural networks over several time-series datasets that are simulated as streams. The obtained results indicate that convolutional architectures achieve a higher performance in terms of accuracy and efficiency.Comment: Paper submitted to the 15th International Conference on Soft Computing Models in Industrial and Environmental Applications (SOCO 2020

Subfunctionalization reduces the fitness cost of gene duplication in humans by buffering dosage imbalances

<p>Abstract</p> <p>Background</p> <p>Driven essentially by random genetic drift, subfunctionalization has been identified as a possible non-adaptive mechanism for the retention of duplicate genes in small-population species, where widespread deleterious mutations are likely to cause complementary loss of subfunctions across gene copies. Through subfunctionalization, duplicates become indispensable to maintain the functional requirements of the ancestral locus. Yet, gene duplication produces a dosage imbalance in the encoded proteins and thus, as investigated in this paper, subfunctionalization must be subject to the selective forces arising from the fitness bottleneck introduced by the duplication event.</p> <p>Results</p> <p>We show that, while arising from random drift, subfunctionalization must be inescapably subject to selective forces, since the diversification of expression patterns across paralogs mitigates duplication-related dosage imbalances in the concentrations of encoded proteins. Dosage imbalance effects become paramount when proteins rely on obligatory associations to maintain their structural integrity, and are expected to be weaker when protein complexation is ephemeral or adventitious. To establish the buffering effect of subfunctionalization on selection pressure, we determine the packing quality of encoded proteins, an established indicator of dosage sensitivity, and correlate this parameter with the extent of paralog segregation in humans, using species with larger population -and more efficient selection- as controls.</p> <p>Conclusions</p> <p>Recognizing the role of subfunctionalization as a dosage-imbalance buffer in gene duplication events enabled us to reconcile its mechanistic nonadaptive origin with its adaptive role as an enabler of the evolution of genetic redundancy. This constructive role was established in this paper by proving the following assertion: <it>If subfunctionalization is indeed adaptive, its effect on paralog segregation should scale with the dosage sensitivity of the duplicated genes</it>. Thus, subfunctionalization becomes adaptive in response to the selection forces arising from the fitness bottleneck imposed by gene duplication.</p

Even after armed conflict, the environmental quality of Indigenous Peoples' lands in biodiversity hotspots surpasses that of non-Indigenous lands

Unidad de excelencia María de Maeztu CEX2019-000940-MIndigenous Peoples lands cover over a fifth of the world's land surface and support high levels of biodiversity. However, for centuries Indigenous Peoples have suffered from deprivation, often dispossession, and even cultural genocide, a process continuing today in some regions. Biodiversity hotspots, global areas of high endemicity that are heavily threatened by habitat loss and other human activities are also affected by conflict. Although covering only 2.4 % of the world's surface, over 80 % of armed conflicts occurred in biodiversity hotspots between 1950 and 2000. Given that many hotspots overlap with Indigenous Peoples' lands, we asked whether the co-occurrence of Indigenous Peoples' lands and high ecological integrity, measured by using Intact Forest Landscapes as units which still contain significant biological diversity, and the Human Footprint as a proxy for anthropogenic impacts, increased the persistence of biodiversity in hotspots where there has been armed conflict. Our results show that, withinbiodiversity hotspots, armed conflict was more likely to occur on Indigenous Peoples' lands than non-Indigenous lands, yet environmental damage and anthropogenic impacts were both lower. We suggest that Indigenous Peoples have been able to moderate ecosystem degradation processes before, during, and after armed conflict because of their strong ties to their lands and their determination to defend their rights and territories. We argue that recognition and support for the efforts of Indigenous Peoples to protect their lands is not only socially just but also essential for meeting the now pressing global post-2020 conservation targets

Contact-free scanning and imaging with the scanning ion conductance microscope

Scanning ion conductance microscopy (SICM) offers the ability to obtain very high resolution topographical images of living cells. In addition, the probe can be used to measure cell responses such as muscle contraction or to map ion channel activity to specific subcellular locations. For biological imaging one of the great advantages of SICM lies in its ability to perform contact-free scanning; imaging cells or tissues without touching the cell surface. However, it is not yet clear when the requirements of this scan mode are met. We have used finite element modelling (FEM) to examine the conditions for contact free scanning and we have validated our modelling using both experimental data and by comparing our results to predictions in analytically tractable situations. Our findings provide a framework for understanding the conditions for contact-free scanning and also extend previous findings with regard to SICM resolution. Finally, we demonstrate the importance of our findings by imaging cells under a variety of conditions

Untargeted lipidomics uncovers lipid signatures distinguishing severe versus moderate forms of acutely decompensated cirrhosis

BACKGROUND AND AIM: Acutely decompensated of cirrhosis is a heterogeneous clinical entity associated with moderate mortality. In some patients, this condition develops quickly into a more often deadly acute-on-chronic liver failure (ACLF), in which other organs such as the kidneys or brain fail. The aim of this study was to characterize the blood lipidome in a large series of patients with cirrhosis and identify specific signatures associated with acute decompensation and ACLF development. METHODS: Serum untargeted lipidomics was performed in 561 patients with acutely decompensated (AD) cirrhosis (518 without and 43 with ACLF) (discovery cohort) and in 265 AD patients (128 without and 137 with ACLF) in whom serum samples were available to perform repeated measurements during the 28-day follow-up (validation cohort). Analyses were also performed in 78 AD patients included in a therapeutic albumin trial, 43 patients with compensated cirrhosis and 29 healthy subjects. RESULTS: The circulating lipid landscape associated with cirrhosis was characterized by a generalized suppression, which was more manifest during acute decompensation and in non-surviving patients. By computing discriminating accuracy and the variable importance projection score for each of the 223 annotated lipids, we identified a sphingomyelin fingerprint specific for AD cirrhosis and a distinct cholesteryl ester and lysophosphatidylcholine fingerprint for ACLF. Liver dysfunction, mainly, and infections were the principal net contributors to these fingerprints, which were dynamic and interchangeable between AD patients whose condition worsened to ACLF and those who improved. Notably, blood lysophosphatidylcholine levels increased in these patients after albumin therapy. CONCLUSIONS: Our findings provide insights into the lipid landscape associated with decompensation of cirrhosis and ACLF progression and identify unique noninvasive diagnostic biomarkers of advanced cirrhosis. LAY SUMMARY: Analysis of lipids in blood from patients with advanced cirrhosis reveals a general suppression of their levels in the circulation of these patients. A specific group of lipids known as sphingomyelins are useful to distinguish compensated from decompensated patients with cirrhosis. Another group of lipids designated cholesteryl esters further distinguish patients with decompensated patients who are at risk of developing organ failures

Identification of a Simple Sequence Repeat molecular-marker set for large-scale analyses of pear germplasm

Simple Sequence Repeats (SSR) are molecular markers suitable to assess the genetic variation of germplasm resources; however, large-scale SSR use requires protocol optimization. The present work aimed to identify SSR markers, developed for pear and other fruit species that are effective in characterizing pear germplasm collections and in demonstrating their use in providing support for genetic breeding programs. From a total of 62 SSR markers investigated, 23 yielding reproducible and polymorphic patterns were used to genotype a sample of 42 pear accessions of the Brazilian Pear Germplasm Bank (PGB). When compared to these 23 SSR markers, a subset of eleven markers, selected based on He, PIC and PId, was used to distinguish individual accessions and perform cluster analysis with similar efficacy. Genetic diversity analysis clustered the European, Japanese and Chinese accessions in distinct groups. This markers subset constitutes a valuable tool for several applications related to pear genetic resources management and breeding

Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies

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