Miracle-dz/UniFAR-FTUs huggingface dataset:
The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ∼13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator.
Open Access Research Article

article distributed under the terms of the Creative Commons At-tribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Allopolyploid speciation and ongoing backcrossing between diploid progenitor and tetraploid progeny lineages in the Achillea millefolium species complex: analyses of single-copy nuclear genes and genomic AFLP Abstract Background: In the flowering plants, many polyploid species complexes display evolutionary radiation. This could be facilitated by gene flow between otherwise separate evolutionary lineages in contact zones. Achillea collina is a widespread tetraploid species within the Achillea millefolium polyploid complex (Asteraceae-Anthemideae). It is morphologically intermediate between the relic diploids, A. setacea-2x in xeric and A. asplenifolia-2x in humid habitats, and often grows in close contact with either of them. By analyzing DNA sequences of two single-copy nuclear genes and the genomic AFLP data, we assess the allopolyploid origin of A. collina-4x from ancestors corresponding to A. setacea-2x and A. asplenifolia-2x, and the ongoing backcross introgression between these diploid progenitor and tetraploid progeny lineages. Results: In both the ncpGS and the PgiC gene tree, haplotype sequences of the diploid A. setacea-2x and A. asplenifolia-2x group into two clades corresponding to the two species, though lineage sorting seems incomplete for the PgiC gene. In contrast, A. collina-4x and its suspected backcross plants show homeologous gene copies: sequences from the same tetraploid individual plant are placed in both diploid clades. Semi-congruent splits of an AFLP Neighbor Net link not only A. collina-4x to both diploid species, but some 4x individuals in a polymorphic population with mixed ploidy levels to A. setacea-2x on one hand and to A. collina-4x on the other, indicating allopolyploid speciation as well as hybridization across ploidal levels. Conclusions: The findings of this study clearly demonstrate the hybrid origin of Achillea collina-4x, the ongoing backcrossing between the diploid progenitor and their tetraploid progeny lineages. Such repeated hybridizations are likely the cause of the great genetic and phenotypic variation and ecological differentiation of the polyploid taxa in Achillea millefolium agg. Background According to the genealogical species concept, species are defined as multi-locus "genotypic clusters" that remain distinct even in the presence of gene flow among each other [1-3]. "Hybridization is thus a normal feature of species biology" [1]. Hybridization and its results, e.g.,
First-Line Antimicrobial Resistance Patterns of Escherichia coli in Children With Urinary Tract Infection in Emergency Department and Primary Care Clinics

Objective: To identify risk factors for antibiotic resistance to Escherichia coli (E. coli) in children with urinary tract infections (UTIs) in emergency room and primary care clinics. Method: This is a cross-sectional study of children 0 to 18 years of age reported to have E coli–positive UTIs whose medical and laboratory records were systematically reviewed. Result: Compared with girls, boys were 2.29 times (confidence interval [CI] = 1.30-4.02) more likely to have E coli isolates resistant to ampicillin and 2 times more likely (CI = 1.13-3.62) to have isolates resistant to trimethoprim-sulfamethoxazole (TMP/SMX). Patients with genitourinary abnormalities were 1.57 times more likely to be resistant to ampicillin (CI = 1.03-2.41) and 1.86 times to TMP/SMX (CI = 1.18-2.94). Conclusion: Higher rates of ampicillin and TMP/SMX resistant urinary E coli isolates were observed among boys and children with a history of genitourinary abnormality. Age and recent antibiotic prescription are also potential risk factors for resistance.
Themis: A participatory navigation system for balanced traffic routing

Navigators based on real-time traffic achieve suboptimal results since, in face of congestion, they greedily shift drivers to currently light-traffic roads and cause new traffic jams. This paper presents Themis, a participatory system navigating drivers in a balanced way. By analyzing time-stamped position reports and route decisions collected from the Themis application, the Themis server estimates both the current traffic rhythm and future traffic distributions. According to the estimated travel time and a popularity score computed using the learned information, Themis coordinates traffic between alternatives and proactively alleviates congestions. Themis has been implemented and its performance has been evaluated at different penetration rates based on real data. Experiments using data from 26,000 taxis demonstrate that Themis reduces both traffic congestions and average travel time at various penetration rates as low as 7%.
Abnormal monocyte recruitment and collateral artery formation in monocyte chemoattractant protein-1 deficient mice

Monocyte chemoattractant protein 1 (MCP-1) has been shown to be effective for the stimulation of collateral artery formation in small and large animal models. The availability of a genetic knockout mouse enables evaluation of the importance of the role of MCP-1 in the natural course of collateral artery growth. In a total of 21 MCP-1 = as well as 13 of the appropriate genetic background controls (f129Sv=JXC57Bl=6JgF1), a femoral artery ligation was performed. Subsequently, a polyethylene catheter, connected to an osmotic minipump, was inserted retrogradely into the occluded femoral artery with the tip pointing upstream. Using this technique, PBS (MCP-1 =: n 1/4-13 and C57Bl=6J: n 1/4-13) or MCP-1 (JE; MCP-1 =: n 1/4-8) was delivered intra-arterially. Seven days after ligation, determination of hind limb flow was assessed by controlled tissue perfusion using differently labeled fluorescent microspheres. MCP-1 = mice exhibited a reduction of hind limb flow of 32.9-9.2% of the unligated hind limb, compared with 55.4-6.8% in C57Bl=6J mice (p <0.01). MCP-1= mice that underwent a subsequent ‘rescue’ treatment with MCP-1 showed a restoration of flow to a level of 47.4-9.8% (p 1/4 NS compared with PBS-treated C57Bl/6J). Specific immunohistochemical staining for monocytes (MOMA-2: MCP-1 =, n 1/4-5 and C57Bl/6J, n 1/4-5) showed a reduced number of monocytes around developing collateral arteries in the MCP-1 = mice. In conclusion, our data show that the absence of MCP-1 causes a strong reduction in flow restoration after femoral artery occlusion, coinciding with a reduced monocyte attraction, emphasizing the central role of this chemokine in the multifactorial process of collateral artery formation.
Linguistic Landscape and Reflection of Chinese Cultural Elements: A Diachronic Study

This paper explores the Chinese cultural elements reflected on the linguistic landscape in a multi-lingual community in a Federal Territory in Malaysia. The main aim of this paper is to examine the notions of linguistic landscape, language practice and Chinese cultural elements. This qualitative research applied linguistic landscape of Ben-Rafael (2009) to unveil the Chinese cultural elements reflected through naming the companies. Two sets of corpora data which were collected in the years of 2011 and 2017 with 212 and 233 brand names respectively. Comparison of Chinese lexis used on the brand names of companies showed the dialect related element is not reflected in the corpus data of 2017 and the additional Chinese cultural elements of concept of direction, numbers and concept of beauty are reflected. The Chinese cultural elements which showed in both data (2011 and 2017) are i) good wishes, ii) name of places, iii) surnames and names, iv) advocating Confucianism and v) dragon, phoenix and tiger.
Aortic pulse wave velocity results depend on which carotid artery is used for the measurements

Objective: Aortic pulse wave velocity (aPWV) is a gold standard noninvasive marker of arterial stiffness. aPWV is usually obtained as carotid–femoral pulse wave velocity by measurements on the common carotid artery and the femoral artery. The carotid arteries branch slightly differently from the aorta towards the right and left side of the neck. Theoretically, using the right or left carotid artery could influence aPWV results and there are no clear guidelines to support the choice of side. The aim of this study was to investigate whether aPWV results depend on right or left side carotid artery measurements in a group of healthy individuals. Methods and results: Two different observers examined 50 individuals without known cardiovascular disease between 23 and 66 years of age. The measurements were performed with the SphygmoCor equipment using both right and left carotid arteries. We found that use of the right carotid artery provided significantly higher aPWV values compared with the left carotid artery, also when using different methods to estimate the travel length of the pulse wave (pooled data, subtracted distance: 0.2 ± 0.4 m/s, P = 0.003; direct distance: 0.2 ± 0.5 m/s, P = 0.001). Conclusion: Using right or left carotid artery affects aPWV, as right-side measurements provided higher values. Attention to this side difference and use of the same carotid artery will increase the strength of intervention studies using aPWV as a surrogate endpoint.
Aging‐Related Decline of Glutathione Peroxidase 3 and Risk of Cardiovascular Events in Patients With Atrial Fibrillation

Background Experimental studies demonstrated that glutathione peroxidase 3 (GPx3), an antioxidant enzyme that catabolizes hydrogen peroxide, protects against thrombosis. Little is known about its role in cardiovascular disease. Methods and Results A prospective cohort study was conducted in 909 atrial fibrillation patients. Serum activities of GPx3, superoxide dismutase (SOD), and catalase were measured at baseline to assess the risk of cardiovascular events during a mean follow‐up of 43.4 months (3291 person‐years). Serum Nox2 and urinary excretion of 11‐deydro‐thromboxane B2 were also measured. During follow‐up 160 cardiovascular events occurred (4.9%/year). Significantly lower values of GPx3 (P<0.001) and SOD (P=0.037) were detected in patients with, compared to those without, cardiovascular events. A lower survival rate was observed in patients with GPx3 (P<0.001) and SOD (P=0.010) activities below the median, as compared to those above. In a fully adjusted Cox regression model, GPx3 was the only antioxidant enzyme predictor of cardiovascular events (hazard ratio 0.647, 95% confidence interval 0.524‐0.798, P<0.001). GPx3 was inversely associated with urinary 11‐dehydro‐thromboxane B2 (B −0.337, P<0.001) and serum Nox2 (B: −0.423, P<0.001). GPx3 activity progressively decreased with decades of age (P<0.001), with a progressive reduction in people aged ≥70 years. Conclusions This study provides evidence that a low antioxidant status, as depicted by reduced levels of GPx3, increases the risk of cardiovascular events in patients with atrial fibrillation. The age‐related decline of GPx3 may represent a mechanism for the enhanced cardiovascular risk in the elderly population.
Simics: A Full System Simulation Platform

Full system simulation seeks to strike a balance between accuracy and performance. Many of its possibilities have been obvious to practitioners in both academia and industry for quite some time, perhaps decades, but Simics supports more of these possibilities within a single framework than other tools do. Simics is a platform for full system simulation that can run actual firmware and completely unmodified kernel and driver code. It is sufficiently abstract to achieve tolerable performance levels, and it provides both functional accuracy for running commercial workloads and sufficient timing accuracy to interface to detailed hardware models. Simics can also run a heterogeneous network of systems from different vendors within the same framework. Exceptionally fast, Simics can easily add new components and leverage older ones within a practical abstraction level. It offers a platform with a rich API and a powerful scripting environment for use in a broad range of applications.
Peak shaving through closed-loop optimization applied to machine tools with periodic behaviour

This paper deals with machine tools characterized by a periodic behaviour and high-power peaks that require an oversized electrical network and cause high costs because electrical utilities charge greatly each power peak. To solve this issue, a new peak-shaving methodology is proposed based on polynomial models and optimization, to reduce the power-consumption peaks height in machine tools with periodic behaviour. A test-bench that emulates the electrical behaviour of a machine tool is used in order to test the proposed method with real data. In the scenarios simulated, the peak height has been reduced between 35% and 15%.
Multi-Domain Adaptive Learning Based on Feasibility Splitting and Adaptive Projected Subgradient Method

We propose the multi-domain adaptive learning that enables us to find a point meeting possibly time-varying specifications simultaneously in multiple domains, e.g. space, time, frequency, etc. The novel concept is based on the idea of feasibility splitting—dealing with feasibility in each individual domain. We show that the adaptive projected subgradient method (Yamada, 2003) realizes the multi-domain adaptive learning by employing (i) a projected gradient operator with respect to a 'fixed' proximity function reflecting the time-invariant specifications and (ii) a subgradient projection with respect to 'time-varying' objective functions reflecting the time-varying specifications. The resulting algorithm is suitable for real-time implementation, because it requires no more than metric projections onto closed convex sets each of which accommodates the specification in each domain. A convergence analysis and numerical examples are presented.
MODELING AND VISUALIZATION OF LANDSCAPE AND OBJECTS USING MULTI-RESOLUTION IMAGE DATA

In this paper we present the photogrammetric modeling and visualization of the UNESCO World Heritage site of Bamiyan, Afghanistan using multi-temporal and multi-resolution images. The final goal of our work is the production of virtual flights over the Bamiyan area, the extraction of cartographic vector features around the village and the documentation of the protected area with a tourist and cultural information system. Each data set was processed with our own photogrammetric software and afterwards the recovered 3D datasets were all merged together. The fusion of the available data is a very complex and critical task, requiring smart algorithms for modeling and visualization. A factor 400 is present between the different resolution levels of the geometry, while, in the texture, we have a factor 1250. Problems with interactive and real-time navigation of large data sets will be also addressed in the paper.
Mechanisms of Receptor‐Mediated Nuclear Import and Nuclear Export

Nuclear transport of proteins and RNA occurs through the nuclear pore complex and is mediated by a superfamily of transport receptors known collectively as karyopherins. Karyopherins bind to their cargoes by recognition of specific nuclear localization signals or nuclear export signals. Transport through the nuclear pore complex is facilitated by transient interactions between the karyopherins and the nuclear pore complex. The interactions of karyopherins with their cargoes are regulated by the Ras‐related GTPase Ran. Ran is assisted in this process by proteins that regulate its GTPase cycle and subcellular localization. In this review, we describe several of the major transport pathways that are conserved in higher and lower eukaryotes, with particular emphasis on the role of Ran. We highlight the latest advances in the structure and function of transport receptors and discuss recent examples of steroid hormone receptor import and regulation by signal transduction pathways. Understanding the molecular basis of nuclear transport may provide insight into human diseases by revealing how nucleocytoplasmic trafficking regulates protein activity.
Survey: image encryption using Salsa20

In present times, multimedia protection is becoming increasingly jeopardized. Therefore numerous ways of protecting information are being utilized by individuals, businesses, and governments. In this paper, we survey Salsa20 as a method for protecting the distribution of digital images in an efficient and secure way. So, we performed a series of tests and some comparisons to justify salsa20 efficiency for image encryption. These tests included visual testing, key space analysis, histogram analysis, information entropy, encryption quality, correlation analysis, differential analysis, sensitivity analysis and performance analysis. Simulation experiment has validated the effectiveness of the Salsa20 scheme for image encryption.
Scenarios for Pollinator Habitat at Denver International Airport

7 Introduction 8 Reserach Goals 12 Literature Review 13 The Shortgrass Prairie Ecosystem 13 Airport Impacts on Ecosystems 14 Airport Case Study: Airport City and Habitat Commitment 15 Airport City 16 Environmental Commitment to Pollinator Habitats 16 Pollinator Conservation Strategies 19 Pollinators of the Denver Region 20 Bees 20 Butterflies 24 Moths 26 Climate Change Resilience 28 Research Methods 30 Using a Normative Scenario Approach 30 Normative Scenario Framework of the Study 32 Past and Present Landscape 36 Functional Components 36 Connectivity 38 Land use and Landcover 40 Ecological Considerations 42 Hypotheses of Desirable Landscape Patterns 44 Airport City 44 Pollinator Habitat 46 Assumptions Across All Scenarios 47 Alternative Landscape Futures 48 Airport City Scenarios 49 Scenario Performance Hypotheses 49 Development Pattern 58 Landscape Element Typologies 60 Table of
A Guide to the Mizar Soft Type System

Introduction Mizar [1, 3] is in a way both typed and untyped. In a foundational sense, Mizar is based on untyped set theory. The set-theoretical world initially consists of many objects of “just one type”. However, the objects can have various properties (a number, ordinal number, complex number, Conway number, a relation, function, complex function, complex matrix), however none of them is considered to be of “foundational importance”, and all these properties are treated as equal “adjectives” or “attributes”, which are semantically just (dependent) predicates. Typically, mathematicians are interested only in some particular properties of the objects, and fluently shift and focus between them, and take some of them as granted in various contexts. Thus, the set of natural numbers can once be treated as a measurable cardinal, another time as a subset of real (and thus “obviously” complex) numbers. A group can simultaneously be a subgroup of other groups. The Mizar “typing” mechanisms are concerned with providing such fluid and “obvious” treatment of the concepts, once the particular relations have been established in the underlying logic. This is especially important in large mathematical theories, where complicated and unpredictable hierarchies (ontologies) between the defined concepts arise, and it is often impossible to pre-design a “perfect type system” between the objects, that would specify upfront all the disjointness, inclusion, and other relations. An important part of the Mizar typing mechanisms is thus dynamic type change. There have been numerous attempts to reconstruct elements of this type system in order to translate the mathematical data encoded in the Mizar language into other common mathematical data exchange formats like OMDoc [4], other proof assistants like HOL Light [6] or Isabelle [5]. The soft-typing mechanisms of Mizar have been actively used in MML already before 1990, i.e., before languages like Haskell started to be developed and provided motivation for the recent soft-typing (“type-class”) mechanisms in systems like Coq and Isabelle. A particular advantage of the soft-typing approach is its straightforward translation to first-order ATP formats. This enabled the first encouraging ATP experiments over the whole Mizar library [8], leading to the expansion of hammer-style ITP methods in the last decade.