Miracle-dz/UniFAR-FTUs huggingface dataset:
BREX is a novel phage resistance system widespread in microbial genomes

The perpetual arms race between bacteria and phage has resulted in the evolution of efficient resistance systems that protect bacteria from phage infection. Such systems, which include the CRISPR‐Cas and restriction‐modification systems, have proven to be invaluable in the biotechnology and dairy industries. Here, we report on a six‐gene cassette in Bacillus cereus which, when integrated into the Bacillus subtilis genome, confers resistance to a broad range of phages, including both virulent and temperate ones. This cassette includes a putative Lon‐like protease, an alkaline phosphatase domain protein, a putative RNA‐binding protein, a DNA methylase, an ATPase‐domain protein, and a protein of unknown function. We denote this novel defense system BREX (Bacteriophage Exclusion) and show that it allows phage adsorption but blocks phage DNA replication. Furthermore, our results suggest that methylation on non‐palindromic TAGGAG motifs in the bacterial genome guides self/non‐self discrimination and is essential for the defensive function of the BREX system. However, unlike restriction‐modification systems, phage DNA does not appear to be cleaved or degraded by BREX, suggesting a novel mechanism of defense. Pan genomic analysis revealed that BREX and BREX‐like systems, including the distantly related Pgl system described in Streptomyces coelicolor, are widely distributed in ~10% of all sequenced microbial genomes and can be divided into six coherent subtypes in which the gene composition and order is conserved. Finally, we detected a phage family that evades the BREX defense, implying that anti‐BREX mechanisms may have evolved in some phages as part of their arms race with bacteria.
Metagenomics Response of Anaerobic Ammonium Oxidation (anammox) Bacteria to Bio-Refractory Humic Substances in Wastewater

Anammox-based processes have been widely applied for the treatment of wastewater (e.g., wastewater irrigation systems and constructed wetland) which consists of bio-refractory humic substances. Nonetheless, the impacts of bio-refractory humic substances on anammox consortia are rarely reported. In the present study, three identical lab-scale anammox reactors (i.e., HS0, HS1 and HS10), two of which were dosed with humic substances at 1 and 10 mg·L−1, respectively, were operated for nearly one year. The long-term operation of the reactors showed that the presence of humic substances in influent had no significant influence on nitrogen removal rates. Despite this, comparative metagenomics showed changes in anammox microbiota structure during the exposure to humic substance; e.g., the relative abundance of Candidatus Kuenenia was lower in HS10 (18.5%) than that in HS0 (22.8%) and HS1 (21.7%). More specifically, a lower level of humic substances (1 mg·L−1) in influent led to an increase of genes responsible for signal transduction, likely due to the role of humic substances as electron shuttles. In contrast, a high level of humic substances (10 mg·L−1) resulted in a slight decrease of functional genes associated with anammox metabolism. This may partially be due to the biodegradation of the humic substances. In addition, the lower dosage of humic substances (1 mg·L−1) also stimulated the abundance of hzs and hdh, which encode two important enzymes in anammox reaction. Overall, this study indicated that the anammox system could work stably over a long period under humic substances, and that the process was feasible for leachate treatment.
Probabilistic Optical Flow Estimation for Large Pixel Displacements Utilizing Egomotion Flow Compensation

The pixel movements in an image sequence grabbed by a camera that is mounted on a mobile platform comprise the superposition of several motion components. These motion components are caused by the egomotion of the camera and by the different movements of the objects seen by the camera. Utilizing sensory information from a calibrated stereo rig and egomotion measurements of the mobile platform we develop a probabilistic framework that estimates optical flow relative to the visual flow induced by the egomotion. Despite rapid egomotion changes and a large range of pixel movements the proposed Dynamic Bayesian Network allows to infer the optical flow induced by moving objects. This is used to segregate moving individuals from static background while the stereo rig is moving. We present optical flow and figure-background segmentation results by applying this general framework to image sequences captured by the humanoid robot ASIMO while he is walking and observing moving people.
Community adaptation to climate change: An exploration of climate change adaptation planning in British Columbia.

Planners in British Columbia must adapt to climate change by preparing for expected and unexpected changes in their communities. The results of survey and workshop research conducted at the Planning Institute of BC conference indicate that planners do not have a high level of knowledge of climate change adaptation. Planners feel that the impacts that will affect BC the most in 50 years will be related to forests, agriculture, river flooding, transportation and water. Different regions in the province will be affected in different ways, and adaptation strategies must be created for the specific needs and attributes of a community. Open-structured workshops are a good method to educate planners about climate change adaptation however, they should not be expected to yield results that can be incorporated into planning documents. Global climate models are a valuable tool that decision makers can use to help determine appropriate planning actions. --P. ii.
Keyword clustering for automatic categorization

Processing short texts is becoming a trend in information retrieval. Since the text has rarely external information, it is more challenging than document. In this paper, keyword clustering is studied for automatic categorization. To obtain semantic similarity of the keywords, a broad-coverage lexical resource WordNet is employed. We introduce a semantic hierarchical clustering. For automatic keyword categorization, a validity index for determining the number of clusters is proposed. The minimum value of the index indicates the potentially appropriate categorization. We show the result in experiments, which indicates the index is effective.
Trend analysis of fire season length and extreme fire weather in North America between 1979 and 2015

We have constructed a fire weather climatology over North America from 1979 to 2015 using the North American Regional Reanalysis dataset and the Canadian Fire Weather Index (FWI) System. We tested for the presence of trends in potential fire season length, based on a meteorological definition, and extreme fire weather using the non-parametric Theil–Sen slope estimator and Mann–Kendall test. Applying field significance testing (i.e. joint significance of multiple tests) allowed the identification of the locations of significant trends, taking into account spatial correlations. Fire season length was found to be increasing over large areas of North America, especially in eastern Canada and the south-western US, which is consistent with a later fire season end and an earlier fire season start. Both positive and negative trends in potential fire spread days and the 99th percentile of FWI occurred in Canada and the contiguous United States, although the trends of largest magnitude and statistical significance were mostly positive. In contrast, the proportion of trends with significant decreases in these variables were much lower, indicating an overall increase in extreme fire weather. The smaller proportion of significant positive trends found over Canada reflects the truncation of the time series, necessary because assimilation of precipitation observations over Canada ceased in the reanalysis post-2002.
Depth-Related Effects on a Meiofaunal Community Dwelling in the Periphyton of a Mesotrophic Lake

Periphyton is a complex assemblage of micro- and meiofauna embedded in the organic matrix that coats most submerged substrate in the littoral of lakes. The aim of this study was to better understand the consequences of depth-level fluctuation on a periphytic community. The effects of light and wave disturbance on the development of littoral periphyton were evaluated in Lake Erken (Sweden) using an experimental design that combined in situ shading with periphyton depth transfers. Free-living nematodes were a major contributor to the meiofaunal community. Their species composition was therefore used as a proxy to distinguish the contributions of light- and wave-related effects. The periphyton layer was much thicker at a depth of 30 cm than at 200 cm, as indicated by differences in the amounts of organic and phototrophic biomass and meiofaunal and nematode densities. A reduction of the depth-level of periphyton via a transfer from a deep to a shallow location induced rapid positive responses by its algal, meiofaunal, and nematode communities. The slower and weaker negative responses to the reverse transfer were attributed to the potentially higher resilience of periphytic communities to increases in the water level. In the shallow littoral of the lake, shading magnified the effects of phototrophic biomass erosion by waves, as the increased exposure to wave shear stress was not compensated for by an increase in photosynthesis. This finding suggests that benthic primary production will be strongly impeded in the shallow littoral zones of lakes artificially shaded by construction or embankments. However, regardless of the light constraints, an increased exposure to wave action had a generally positive short-term effect on meiofaunal density, by favoring the predominance of species able to anchor themselves to the substrate, especially the Chromadorid nematode Punctodora ratzeburgensis.
In Vitro- and In Vivo-Generated Defective RNAs of Satellite Panicum Mosaic Virus Define cis-Acting RNA Elements Required for Replication and Movement

ABSTRACT Satellite panicum mosaic virus (SPMV) depends on its helper virus, panicum mosaic virus (PMV), to provide trans-acting proteins for replication and movement. The 824-nucleotide (nt) genome of SPMV possesses an open reading frame encoding a 17.5-kDa capsid protein (CP), which is shown to be dispensable for SPMV replication. To localize cis-acting RNA elements required for replication and movement, a comprehensive set of SPMV cDNA deletion mutants was generated. The results showed that the 263-nt 3′ untranslated region (UTR) plus 73 nt upstream of the CP stop codon and the first 16 nt in the 5′ UTR are required for SPMV RNA amplification and/or systemic spread. A region from nt 17 to 67 within the 5′ UTR may have an accessory role in RNA accumulation, and a fragment bracketing nt 68 to 104 appears to be involved in the systemic movement of SPMV RNA in a host-dependent manner. Unexpectedly, defective RNAs (D-RNAs) accumulated de novo in millet plants coinfected with PMV and either of two SPMV mutants: SPMV-91, which is incapable of expressing the 17.5-kDa CP, and SPMV-GUG, which expresses low levels of the 17.5-kDa CP. The D-RNA derived from SPMV-91 was isolated from infected plants and used as a template to generate a cDNA clone. RNA transcripts derived from this 399-nt cDNA replicated and moved in millet plants coinoculated with PMV. The characterization of this D-RNA provided a biological confirmation that the critical RNA domains identified by the reverse genetic strategy are essential for SPMV replication and movement. The results additionally suggest that a potential “trigger” for spontaneous D-RNA accumulation may be associated with the absence or reduced accumulation of the 17.5-kDa SPMV CP. This represents the first report of a D-RNA associated with a satellite virus.
Amelioration of Acute Kidney Injury in Lipopolysaccharide-Induced Systemic Inflammatory Response Syndrome by an Aldose Reductase Inhibitor, Fidarestat

Background Systemic inflammatory response syndrome is a fatal disease because of multiple organ failure. Acute kidney injury is a serious complication of systemic inflammatory response syndrome and its genesis is still unclear posing a difficulty for an effective treatment. Aldose reductase (AR) inhibitor is recently found to suppress lipopolysaccharide (LPS)-induced cardiac failure and its lethality. We studied the effects of AR inhibitor on LPS-induced acute kidney injury and its mechanism. Methods Mice were injected with LPS and the effects of AR inhibitor (Fidarestat 32 mg/kg) before or after LPS injection were examined for the mortality, severity of renal failure and kidney pathology. Serum concentrations of cytokines (interleukin-1β, interleukin-6, monocyte chemotactic protein-1 and tumor necrosis factor-α) and their mRNA expressions in the lung, liver, spleen and kidney were measured. We also evaluated polyol metabolites in the kidney. Results Mortality rate within 72 hours was significantly less in LPS-injected mice treated with AR inhibitor both before (29%) and after LPS injection (40%) than untreated mice (90%). LPS-injected mice showed marked increases in blood urea nitrogen, creatinine and cytokines, and AR inhibitor treatment suppressed the changes. LPS-induced acute kidney injury was associated with vacuolar degeneration and apoptosis of renal tubular cells as well as infiltration of neutrophils and macrophages. With improvement of such pathological findings, AR inhibitor treatment suppressed the elevation of cytokine mRNA levels in multiple organs and renal sorbitol accumulation. Conclusion AR inhibitor treatment ameliorated LPS-induced acute kidney injury, resulting in the lowered mortality.
Genome-wide identification, isolation and expression analysis of auxin response factor (ARF) gene family in sweet orange (Citrus sinensis)

Auxin response factors (ARFs) are an important family of proteins in auxin-mediated response, with key roles in various physiological and biochemical processes. To date, a genome-wide overview of the ARF gene family in citrus was not available. A systematic analysis of this gene family in citrus was begun by carrying out a genome-wide search for the homologs of ARFs. A total of 19 nonredundant ARF genes (CiARF) were found and validated from the sweet orange. A comprehensive overview of the CiARFs was undertaken, including the gene structures, phylogenetic analysis, chromosome locations, conserved motifs of proteins, and cis-elements in promoters of CiARF. Furthermore, expression profiling using real-time PCR revealed many CiARF genes, albeit with different patterns depending on types of tissues and/or developmental stages. Comprehensive expression analysis of these genes was also performed under two hormone treatments using real-time PCR. Indole-3-acetic acid (IAA) and N-1-napthylphthalamic acid (NPA) treatment experiments revealed differential up-regulation and down-regulation, respectively, of the 19 citrus ARF genes in the callus of sweet orange. Our comprehensive analysis of ARF genes further elucidates the roles of CiARF family members during citrus growth and development process.
Experiments on coordinated motion of aerial robotic manipulators

In this paper a three layer control architecture for multiple aerial robotic manipulators is presented. The top layer, on the basis of the desired mission, determines the end-effector desired trajectory for each manipulator, while the middle layer is in charge of computing the motion references in order to track such end-effectors trajectories coming from the upper layer. Finally the bottom layer is a low level motion controller, which tracks the motion references. The overall mission is decomposed in a set of elementary behaviors which are combined together, through the Null Space-based Behavioral (NSB) approach, into more complex compounds behaviors. The proposed framework has been tested conducting an experimental campaign.
Applying Business Strategy Models in Organizations

Increasing adoption of Open Source Software (OSS) in information system engineering has led to the emergence of different OSS business strate- gies that affect and shape organizations' business models. In order to obtain the specific organizational model for a concrete organization that is adhering to a specific OSS business strategy, we need to instantiate the general knowledge included in this business strategy. This paper describe the process in which this general knowledge is instantiated and define a set of operations over i* models to implement the instantiation concept. Although conceived in the field of OSS, the approach is generalizable to any kind of business strategy.
Fast Heuristics for the QoS Multicast Routing Problem

The NP-hard QoS Multicast Routing (QoSMR) is one of the most challenging problems in recent networks. In this paper, we investigate the QoSMR problem as well as its different existing formulations. We analyze the limitations of these formulations and propose a novel one. The main advantage of our formulation is that it considers not only the quality of the multicast subgraph formed by the computed paths, but also takes into account the end-to-end quality of each of these paths. Moreover, we study the state of the art proposal for solving the QoSMR problem and show that the well-known MAMCRA algorithm can be very expensive in computation time. Therefore, we propose two efficient heuristics based on the computation of shortest paths. Extensive simulations are performed, and obtained results prove that these fast heuristics have bounded computation time and find satisfying solutions for the QoS requirements.
Histopathologic and immunohistochemical comparison of human, rabbit, and swine aneurysms embolized with platinum coils.

BACKGROUND AND PURPOSE The purpose of this study was to clarify the cellular mechanisms of aneurysmal healing by comparing histologic and immunohistochemical findings in experimental rabbit and swine aneurysms to a human aneurysm embolized with platinum coils. METHODS Swine sidewall aneurysms (n = 5, harvested at 12 weeks) and elastase-induced rabbit aneurysms (n = 6, harvested at 24 weeks) were created and embolized. A single human aneurysm, embolized 6 years before death, was harvested following autopsy. All specimens were processed by using a modified paraffin embedding technique. Tissue was sectioned and stained with hematoxylin and eosin and Masson trichrome. Immunohistochemistry and immunofluorescence were performed with multiple antibodies, including alpha smooth muscle actin, myosin heavy chain, desmin, vimentin, and CD31. RESULTS The human aneurysm's dome was filled with loose, hypocellular, amorphous tissue. The aneurysm's neck was completely covered with a thin layer of hypocellular tissue. Collagen and myofibroblasts were sparse in both the dome and neck. Rabbit aneurysms' domes were also filled with a loose, hypocellular tissue, amorphous matrix. In 5 of 6 aneurysms, a thin layer of hypocellular tissue ran along the neck. Collagen and myofibroblasts were sparse in the dome. Swine aneurysms were filled with densely infiltrated tissue, including chronic inflammatory tissue and extensive, attenuated collagen fiber bundles associated with myofibroblasts. Thick layers of myofibroblasts entirely bridged the necks. CONCLUSIONS Absence of collagen deposition and scant myofibroblastic reaction to platinum coil embolization are seen in the rabbit model but not in swine aneurysms. The elastase-induced aneurysm model in rabbits is more suitable than sidewall swine aneurysms for testing of modified devices aimed at improving intra-aneurysmal fibrosis.
Order Independent Switching Operations in Radially Operated Networks

Radially operated networks may be switched to change configuration in order to improve performance. Changing one configuration into another involves finding and sequencing ON/OFF switching steps. This is in general a complex task as the switching step possibilities must be dynamically investigated in order neither to create meshes nor to lose connectivity. In this paper, we propose to represent the switching possibilities by a bipartite graph and propose a procedure to determine maximum cardinality sets of such switching steps that assure radiality and connectivity for all possible switching sequences. The representation and the procedure are illustrated with a practical example.
An Automatic Approach for Service Composition by Mining Process Knowledge from the Web

Current approaches in Service-Oriented Architecture (SOA) are challenging for users to get involved in the service composition due to the in-depth knowledge required for SOA standards and techniques. To shield users from the complexity of SOA standards, we automatically generate composed services for end-users using process knowledge available in the Web. Our approach uses natural language processing techniques to extract tasks. Our approach automatically identifies services required to accomplish the tasks. We represent the extracted tasks in a task model to find the services and then generate a user interface (UI) for a user to perform the tasks. Our case study shows that our approach can extract the tasks from how-to instructions Web pages with high precision (i.e., 90%). The generated task model helps to discover services and compose the found services to perform a task. Our case study shows that our approach can reach more than 90% accuracy in service composition by identifying accurate data flow relation between services.
Estimating loss rates in an integrated services network by neural networks

Loss rate is one of the most important quality of service (QoS) requirements in a packet communication network carrying multimedia traffic. This paper presents a method for estimating loss rates as a function of a feature vector, x, based on a maximum likelihood principle. Two backpropagation networks, a multi-layer perceptron (MLP) network and a radial basis function (RBF) network, are applied to samples of simulated M/M/1 queue data, as well as to samples of simulated combinations of constant bit rate (CBR) and Poisson traffic data, at different x. Our results show that a) this method is superior to earlier methods since it properly treats the samples, eliminating nuisance parameters, b) it gives a direct measure of QoS that can be used in higher level communication network decision functions, and c) RBF networks give more accurate loss rate estimates than MLP networks do.
Nexus: a real time QA system

Factoid Question Answering has attracted much research interest in recent years. The performances of the state of the art factoid QA systems in terms of the correctness of answers seem to be approaching reasonabe level as shown by TREC QA exercises [2] to make Question Answering nearly viable for practical uses. However, one important issue that has attracted less attention is that of whether a QA system can be efficient enough to scale up to the intensive usages such as a web search engine might be subjected to. Unlike web search engines such as Google which can produce results on real time while handling tens of thousands of queries per second, a typical QA system requires several seconds or even minutes to produce the answer to a single question. This, we believe, is due to the fact that a typical QA system performs most of its work on-line after a question has been put. In this demonstration, we present our system, Nexus, which shifts a significant proportion of work off-line by pre-processing and constructing a specialized index for potential answers – currently, expressions bearing named entities such as people, organisations and locations. This substantially increases the system’s speed and efficiency.
Errors in Low and Lapsley's article "Optimization Flow Control, I: Basic Algorithm and Convergence"

In the note two errors in Low and Lapsley's article "Optimization Flow Control, I: Basic Algorithm and Convergence", "IEEE/ACM Transactions on Networking", 7(6), pp. 861-874, 1999, are shown. Because of these errors the proofs of both theorems presented in the article are incomplete and some assessments are wrong.