Numerical investigations are an important research tool in quantum information theory. There already exists a wide range of computational tools for quantum information theory implemented in various ...programming languages. However, there is little effort in implementing this kind of tools in the Julia language. Julia is a modern programming language designed for numerical computation with excellent support for vector and matrix algebra, extended type system that allows for implementation of elegant application interfaces and support for parallel and distributed computing. QuantumInformation.jl is a new quantum information theory library implemented in Julia that provides functions for creating and analyzing quantum states, and for creating quantum operations in various representations. An additional feature of the library is a collection of functions for sampling random quantum states and operations such as unitary operations and generic quantum channels.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Recent years have witnessed an unprecedented increase in experiments and hybrid simulations involving quantum computers. In particular, quantum annealers. There exist a plethora of algorithms ...promising to outperform classical computers in the near-term future. Here, we propose a parallel in time approach to simulate dynamical systems designed to be executed already on present-day quantum annealers. In essence, purely classical methods for solving dynamics systems are serial. Therefore, their parallelization is substantially limited. In the presented approach, however, the time evolution is rephrased as a ground-state search of a classical Ising model. Such a problem is solved intrinsically in parallel by quantum computers. The main idea is exemplified by simulating the Rabi oscillations generated by a two-level quantum system (i.e. qubit) experimentally.
High-order cumulant tensors carry information about statistics of non-normally distributed multivariate data. In this work we present a new efficient algorithm for calculation of cumulants of ...arbitrary orders in a sliding window for data streams. We show that this algorithm offers substantial speedups of cumulant updates compared with the current solutions. The proposed algorithm can be used for processing on-line high-frequency multivariate data and can find applications, e.g., in on-line signal filtering and classification of data streams. To present an application of this algorithm, we propose an estimator of non-Gaussianity of a data stream based on the norms of high order cumulant tensors. We show how to detect the transition from Gaussian distributed data to non-Gaussian ones in a data stream. In order to achieve high implementation efficiency of operations on super-symmetric tensors, such as cumulant tensors, we employ a block structure to store and calculate only one hyper-pyramid part of such tensors.
Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a ...micro-reactor and is a complex structure consisting of several components. It includes the host, its gut microbiome and fungal gardens, in the case of fungi-growing higher termites. The digestive tract of soil-feeding higher termites is characterised by radial and axial gradients of physicochemical parameters (e.g. pH, O
and H
partial pressure), and also differs in the density and structure of residing microbial communities. Although soil-feeding termites account for 60% of the known termite species, their biomass degradation strategies are far less known compared to their wood-feeding counterparts.
In this work, we applied an integrative multi-omics approach for the first time at the holobiont level to study the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis. We relied on 16S rRNA gene community profiling, metagenomics and (meta)transcriptomics to uncover the distribution of functional roles, in particular those related to carbohydrate hydrolysis, across different gut compartments and among the members of the bacterial community and the host itself. We showed that the Labiotermes gut was dominated by members of the Firmicutes phylum, whose abundance gradually decreased towards the posterior segments of the hindgut, in favour of Bacteroidetes, Proteobacteria and Verrucomicrobia. Contrary to expectations, we observed that L. labralis gut microbes expressed a high diversity of carbohydrate active enzymes involved in cellulose and hemicelluloses degradation, making the soil-feeding termite gut a unique reservoir of lignocellulolytic enzymes with considerable biotechnological potential. We also evidenced that the host cellulases have different phylogenetic origins and structures, which is possibly translated into their different specificities towards cellulose. From an ecological perspective, we could speculate that the capacity to feed on distinct polymorphs of cellulose retained in soil might have enabled this termite species to widely colonise the different habitats of the Amazon basin.
Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Miscanthus sp. biomass could satisfy future biorefinery value chains. However, its use is largely untapped due to high recalcitrance. The termite and its gut microbiome are considered the most ...efficient lignocellulose degrading system in nature. Here, we investigate at holobiont level the dynamic adaptation of Cortaritermes sp. to imposed Miscanthus diet, with a long-term objective of overcoming lignocellulose recalcitrance. We use an integrative omics approach combined with enzymatic characterisation of carbohydrate active enzymes from termite gut Fibrobacteres and Spirochaetae. Modified gene expression profiles of gut bacteria suggest a shift towards utilisation of cellulose and arabinoxylan, two main components of Miscanthus lignocellulose. Low identity of reconstructed microbial genomes to closely related species supports the hypothesis of a strong phylogenetic relationship between host and its gut microbiome. This study provides a framework for better understanding the complex lignocellulose degradation by the higher termite gut system and paves a road towards its future bioprospecting.
Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, ...which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge.
We present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented.
VizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux.
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualize its content integrated with omics data and simulation results.
We manually ...drew a comprehensive map, ReconMap 2.0, that is consistent with the content of Recon 2. We present it within a web interface that allows content query, visualization of custom datasets and submission of feedback to manual curators.
ReconMap can be accessed via http://vmh.uni.lu , with network export in a Systems Biology Graphical Notation compliant format released under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. A Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension to interact with ReconMap is available via https://github.com/opencobra/cobratoolbox .
ronan.mt.fleming@gmail.com.
We introduce the model of generalized open quantum walks on networks using the Transition Operation Matrices formalism. We focus our analysis on the mean first passage time and the average return ...time in Apollonian networks. These results differ significantly from a classical walk on these networks. We show a comparison of the classical and quantum behaviour of walks on these networks.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different ...stages of humification. Lignocellulose is often a principal component of such plant diet, and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While lower termites and their gut flagellates were given larger scientific attention in the past, the gut lignocellulolytic bacteria of higher termites remain less explored. Therefore, in this study, we investigated the structure and function of gut prokaryotic microbiomes from 11 higher termite genera representative of Syntermitinae, Apicotermitinae, Termitidae and Nasutitermitinae subfamilies, broadly grouped into plant fibre- and soil-feeding termite categories.
Despite the different compositional structures of the studied termite gut microbiomes, reflecting well the diet and host lineage, we observed a surprisingly high functional congruency between gut metatranscriptomes from both feeding groups. The abundance of transcripts encoding for carbohydrate active enzymes as well as expression and diversity profiles of assigned glycoside hydrolase families were also similar between plant fibre- and soil-feeding termites. Yet, dietary imprints highlighted subtle metabolic differences specific to each feeding category. Roughly, 0.18% of de novo re-constructed gene transcripts were shared between the different termite gut microbiomes, making each termite gut a unique reservoir of genes encoding for potentially industrially applicable enzymes, e.g. relevant to biomass degradation. Taken together, we demonstrated the functional equivalence in microbial populations across different termite hosts.
Our results provide valuable insight into the bacterial component of the termite gut system and significantly expand the inventory of termite prokaryotic genes participating in the deconstruction of plant biomass. Video Abstract.
A 2020 investigation into air quality in urban areas found that nitrogen oxide and PM10 concentrations were above average. With the exception of summer, three seasons were found to have the highest ...nitrogen oxide concentrations, with a significant decrease during COVID-19. The significant PM10 relationship showed how communication affects the worsening of air quality, especially in the winter. The highest concentration of nitrogen oxide of 53.99 µg m−3 indicated the possibility of advection of pollutants from outside the agglomeration. The highest level of nitrogen oxide content, 95.95 µg m−3 in the atmospheric air, confirmed the significant presence of pollutants of communication origin. The advancement of electro-mobility and the application of cutting-edge technologies alongside renewable energy sources may contribute to a decrease in the amount of harmful substances released into the atmosphere.
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