Miracle-dz/UniFAR-FTUs huggingface dataset:
Biology of the ectomycorrhizal genus Rhizopogon. V. Phylogenetic relationships in the Boletales inferred from LSU rDNA sequences

Abstract The phylogenetic relationship between Alpova, Chroogomphus, Gomphidius, Rhizopogon, Suillus, and Truncocolumella and their placement in the Boletales was tested through maximum parsimony analyses of large subunit nuclear ribosomal DNA sequences. Taxon sampling included representatives of the genera Alpova, Boletellus, Boletus, Chroogomphus, Gomphidius, Melanogaster, Paragyrodon, Phylloporus, Rhizopogon, Suillus, Truncocolumella, Tylopilus, and Xerocomus, as well as species from the Agaricales, Russulales, and Polyporales. The order Boletales was strongly supported as monophyletic. Furthermore, within this order, two major groups emerged: the boletoid radiation and a Melanogastraceae/Paragyrodon sphaerosporus paraphyletic assemblage, and the suilloid radiation. The boletoid radiation and a Melanogastraceae/Paragyrodon sphaerosporus assemblage was strongly supported. Although the boletoid radiation was not strongly supported by bootstrap analysis, the clade did not collapse in the strict consensus topology. This clade comprised species from the genera Boletellus, Boletus, Phylloporus, Tylopilus, and Xerocomus. The Boletaceae sensu Singer was not monophyletic. Although species relationships within the boletoid radiation were not well resolved, the genus Boletus did not appear to be monophyletic. Alpova diplophloeus, A. trappei, Melanogaster tuberiformis, and Paragyrodon sphaerosporus formed a paraphyletic assemblage basal to the boletoid radiation clade. The suilloid clade was strongly supported and included Alpova olivaceotinctus, Chroogomphus, Gomphidius, Rhizopogon, Suillus and Truncocolumella citrina. Species in the genus Alpova therefore were grouped both within and outside the suilloid radiation. Within the suilloid radiation, Suillus was inferred to be more closely related to Truncocolumella citrina and the Gomphidiaceae than to Rhizopogon, suggesting a more distant relationship between Suillus and Rhizopogon than previously hypothesized. Rhizopogon was not supported as monophyletic, although its monophyly could not be rejected by the data. Alpova olivaceotinctus grouped within the genus Rhizopogon, consistent with previous classifications, and is returned to that genus.
Program synthesis for combinatorial optimisation problems: Position statement

A high-level abstract-datatype-based constraint modelling language opens the door to an automatable empirical determination -- by a synthesiser -- of how to ’best’ represent the decision variables of a combinatorial optimisation problem, based on (real-life) training instances of the problem. the extreme case where no such training instances are provided, such a synthesiser would simply be non-deterministic. A first-order relational calculus is a good candidate for such a language, as it gives rise to very natural and easy-to-maintain models of combinatorial optimisation problems.
The Neurospora crassa chs3 gene encodes an essential class I chitin synthase

Abstract In Neurospora crassa, at least five different DNA fragments related to chitin synthases have been identified. In this study we have cloned, sequenced, mapped and characterized the chitin synthase 3 structural gene (designated chs3) of N. crassa. Based on the amino acid sequence deduced from the cloned chs3 genomic DNA fragments we have designated this gene as a class I chitin synthase. The chs3 gene is transcribed predominantly at the early stages of mycelial growth and is expressed during all stages of asexual growth. The fact that strains with nuclei harboring a disrupted chs3 gene could only be maintained as heterokaryons indicates that this gene is indispensable in N. crassa.
Penicillium pimiteouiense: a new species isolated from polycystic kidney cell cultures

As part of a study of polycystic kidney dis- ease (PKD), epithelial cells were isolated and propa- gated from cyst walls of human kidneys obtained at nephrectomy. A Penicillium species was found grow- ing with the epithelial cells in some culture flasks. It was monoverticillate and somewhat resembled P res- trictum but differed morphologically from this and all other Penicillium species. Two strains of this fungus were isolated in pure culture and described as the new species Penicillium pimiteouiense. Ochratoxin A production was not detected in P. pimiteouiense. The role, if any, that this fungus plays in polycystic kidney disease is not known.
ONTOGENY OF GLOMUS CLARUM IN RI T-DNA TRANSFORMED ROOTS

The spore ontogeny of Glomus clarum was monitored during the nonsymbiotic growth phase and after the colonization in transformed roots of clover (Trifolium repens) and carrot (Daucus carota). The germinated spore in water agar produced spore- like vesicles during the nonsymbiotic phase. It has been shown that these structures were in factjuvenile spores, that after root colonization were able to form mature spores. G. clarum began the spore formation in its nonsymbiotic phase. However, the juvenile spore structures senesced without establishment of an effective symbiosis. Spores of the genus Glomus are assumed to form terminally from sporogenic hy- phae, but the ontogeny of G. clarum in transformed roots demonstrates that sporogenesis can also involve intercalary sporelike vesicles formed along the spo- rogenic hyphae. Using root organ culture system, all steps of spore formation can be followed in vivo with- out disturbing the system. This technique provides a better way to visualise events that occur during the pre- and postcolonization phase of arbuscular mycor- rhiza, allowing the comprehension of full life cycle of this fungi. There are morphological variations in the ontogeny of G. clarum spores which differentiate
INTERVAL PREDICTION BASED ON EXPERTS' STATEMENTS ∗

In the work (1) we proposed an approach of forming a consensus of experts' statements in pattern recognition. In this paper, we present a method of aggregating sets of individual statements into a collective one for the case of forecasting of quantitative variable. n j = , where the set X may simultaneously contain qualitative and quantitative features j X , n j , 1 = . Let j D be the domain of the feature j X , n j , 1 = , y D be the domain of the feature Y. The feature space is given by the product set ∏ = = n j j D D 1 . In this paper, we consider statements i
Evaluating Infrastructures of the 21st Century City: Informational Cities in Japan as Case Studies

There are many theories and concepts aiming at describing and measuring the modern cities in the 21 st century: digital city, smart city, creative city, knowledge city or global city–each of them with different infrastructure and diverse components. In the present case we combine all these aspects, quantify and measure them under the concept of the informational city. We are using methods of the information science approach on urban studies, including the ethnographic field study, grounded theory method and further research-based proceedings. While looking for informational cities we evaluate as case studies the advancement of four Japanese cities in regard to various aspects and conclude which of them mostly conforms to the expectations of the 21 st century city.
Encephalitozoon cuniculi in Raw Cow's Milk Remains Infectious After Pasteurization

Abstract This study describes the prevalence of Encephalitozoon cuniculi in raw cow's milk and evaluates the effect of different milk pasteurization treatments on E. cuniculi infectivity for severe combined immunodeficient (SCID) mice. Using a nested polymerase chain reaction approach, 1 of 50 milking cows was found to repeatedly shed E. cuniculi in its feces and milk. Under experimental conditions, E. cuniculi spores in milk remained infective for SCID mice following pasteurization treatments at 72°C for 15 s or 85°C for 5 s. Based on these findings, pasteurized cow's milk should be considered a potential source of E. cuniculi infection in humans.
ON THE OBJECT MODELLING OF THE MASSIVELY PARALLEL ARCHITECTURE COMPUTERS

ABSTRACT In this paper, we present a modelling method to describe and emulate the massively parallel single Instruction Multiple Data (SIMD) structure machines. Among the modelled machines, we distinguish the linear, 2D meshes and pyramidal structures. All these computers are based physically on a multitude of fine grained processing elements (PE) arranged and coupled according to their associated topological pattern. Basing on the object modelling technique and on the XML description language, we develop a hard kernel of a parallel 2D virtual machine in which we translate all the physical properties of its different components. This kernel can be easily extended to the other mentioned topological structures. A parallel programming language and its compiler are also developed to edit, compile and run parallel programs. Furthermore, some illustrative examples will be given to show how the developed instruction sets can be manipulated to touch a large field of the parallel data processing applications.
Research and Application of Synchronous Generator Model Based on Simulink

There is no abc axis system model of synchronous generator in the SimPowerSystem (SPS) of Simulink but the model of dq axis system ，and the model of generator in SPS is lack of flexible tuning function of variable. In this paper a model of synchronous generator is established in abc axis system, which is based on the Simulink software. This model is consist of basic calculation module in the Simulink is created to solve the above problems. Using the model simulates a rotating-rectifier brushless synchronous generator system of planes and the simulation results indicate that the model is accurate enough.
Cancer Stem Cells Recapitulates the Heterogeneity of Glioblastomas

Glioblastoma (GBM) tumor is the most aggressive and heterogeneous cancer originating from the Central Nervous System (CNS). It is not clear how this tumor heterogeneity comes about. The cancer stem cells (CSCs) theory dictates that GBM tumors may arise from a small pool of cells that determine the cancer progression. In this work, we demonstrate that isolated CSCs from single GBM- derived neurospheres give rise to several clones with different proliferation rates in vitro. Moreover, the tumors generated by xenografts of these clones, displayed histological features of GBM with different growth rates, which reflect the proliferation kinetics of the injected clones. These results indicate that exist differences in the tumorigenic capacity of CSCs derived from the same single neurosphere, suggesting a possible combination of the cancer stem cells hypothesis and clonal evolution model in generating GBM heterogeneity. We than investigated these differences as possibly related to the distinct expression of transcription factors NRSF/REST and Olig2, the equilibrium of which seems to maintain the more aggressive clone in the more tumorigenic status. Our results indicate a possible predictive role of REST since it is up regulated in more proliferative, invasive and less differentiated cells.
The use of PCR‐DGGE to determine bacterial fingerprints for poultry and red meat abattoir effluent

Strict legislation and chemical composition monitoring of effluent may be useful, but the data generated do not allow for source tracking, and enforcing legislation remains problematic in the South African setting. These difficulties emphasize the necessity for effluent source traceability. Denaturing gradient gel electrophoresis (DGGE) targeting the V3 region of the 16S rRNA gene was considered as fingerprinting technique for effluent originating from abattoirs slaughtering different animal species. The influence of treatment to remove excess fat from effluent prior to molecular analyses and different PCR approaches on the detection of bacterial diversity were considered. Use of a treatment option to remove fat and a nested PCR approach resulted in up to 51% difference in inter‐sample diversity similarity. A robust approach with no pre‐treatment to remove PCR inhibitors, such as fat, and direct amplification from genomic DNA yielded optimal/maximal bacterial diversity fingerprints. Repeatable fingerprints were obtained for poultry abattoir effluent over a 4‐month period, but profiles for the red meat abattoir varied with maximum similarity detected only 33·2%. Genetic material from faecal indicators Aeromona spp and Clostridium spp were detected. Genera unique to each effluent were present; Anoxybacillus, Patulibacter and Oleispira in poultry abattoir effluent and Porphyromonas and Peptostreptococcus in red meat abattoir effluent.
Decreased HDAC1 Gene Expression in Patients with Alzheimer's Disease

KEYWORDS Alzheimer's Disease. HDAC1. mRNA Expression. RT-PCR ABSTRACT One of the commonest neurodegenerative diseases, Alzheimer's disease (AD), is characterized by progressive decline in memory and cognitive functions with inexorable neurodegeneration in brain. Histone-tail acetylation have been known to be associated with some crucial neurologic functions, thus, the enzymes regulating this events such as HDAC1 are associated with such neurodegenerative diseases like AD. The research objective was to document the levels of HDAC1 expression in peripheral lymphocytes harvested from patients clinically diagnosed with AD. Fifty patients diagnosed with AD, and 49 age- and sex-matched controls were recruited to the study. Total RNA was extracted, cDNA was synthesized, and HDAC1 expressions were tested using quantitative real-time polymerase chain reaction (qRT-PCR). HDAC1 expression was found significantly attenuated in patients with AD compared with the controls (p<0.001). The research data suggested that lower expression levels of HDAC1 may have an impact in the etiology or disease course of AD.
Isolation and characterization of lytic bacteriophages as an alternative to prevent pseudomonas spp in poultry industry

The Pseudomonas genus is a big problem mainly for the poultry food industry. The shelf life of chicken carcasses stored under refrigeration is limited by the appearance of undesirable odors and sliminess surface generated primarily by Gram negative bacteria. Due to the subsequent emergence of resistant bacteria, is necessary proving new alternatives as guaranty the microbiological quality of foods and human health. Bacteriophages or phages are viruses of bacteria that use resources of bacteria for their replication and killing bacteria “naturally”, showing them as a potential tool for bacteria biocontrol in food industry. In this study, 11 bacteriophages were isolated from the exudate product of defrost of chicken carcasses using as host strains Pseudomonas aeruginosa (ATCC 25619) and Pseudomonas fluorescens (ATCC 13525). This study also aimed at the purification, quantification and morphological and molecular characterization of phages (RFLP). Bacteriophage can be found in all types of environments, it was possible to perform isolation and purification and achieve concentrations of 1011 PFU/ml, which demonstrated a broad spectrum of action on different bacteria of the family Enterobacteriaceae. Bacteriophages were classified as belonging to the order of Caudovirales and families Podoviridae and Myoviridae. Bacteriophages showed similar morphology, but some showed different genetic profiles. Bacteriophages can be found in the chicken carcasses and the fact that they are regulators of bacterial growth letting their use as antimicrobial agents to prevent spoilage bacteria as P. fluorescens and pathogens as P. aeruginosa as evidenced in this study. So, bacteriophage with specificity for Pseudomonas can be an interesting instrument for promoting the expansion of the shelf life of chicken products due to their ability to infect this microorganism.
The Knowledge Grid:Toward Cyber-Physical Society

The Knowledge Grid is an intelligent and sustainable interconnection environment that consists of autonomous individuals, self-organized semantic communities, adaptive networking mechanisms, evolving semantic link networks keeping meaningful connection between individuals, flows for dynamic resource sharing, and mechanisms supporting effective resource management and providing appropriate knowledge services for learning, innovation, teamwork, problem solving, and decision making. This book presents its methodology, theory, models and applications systematically for the first time. Its second edition fulfills the ideal of the Knowledge Grid by increasing many up-to-date new contents, including: the systematic method of semantic link network that supports uncertainty management, discovery of semantic links and semantic communities, and autonomous semantic data model; semantic peer-to-peer infrastructures for efficient knowledge sharing; and, a new centrality measure of network and its application in e-science. This new edition will undoubtedly provide refreshing materials for researchers, academics, practitioners and students.
Regions and Connections: Complementary Approaches to Characterize Brain Organization and Function

Functional magnetic resonance imaging has proved to be a powerful tool to characterize spatiotemporal patterns of human brain activity. Analysis methods broadly fall into two camps: those summarizing properties of a region and those measuring interactions among regions. Here we pose an unappreciated question in the field: What are the strengths and limitations of each approach to study fundamental neural processes? We explore the relative utility of region- and connection-based measures in the context of three topics of interest: neurobiological relevance, brain-behavior relationships, and individual differences in brain organization. In each section, we offer illustrative examples. We hope that this discussion offers a novel and useful framework to support efforts to better understand the macroscale functional organization of the brain and how it relates to behavior.
A multifunctional co-solvent pair reveals molecular principles of biomass deconstruction.

The complex structure of plant cell walls resists chemical or biological degradation, challenging the breakdown of lignocellulosic biomass into renewable chemical precursors that could support future production of green chemicals and transportation fuels. Here, experimental and computational results reveal how molecular interactions between tetrahydrofuran (THF)-water and lignocellulose can identify this co-solvent pair and other co-solvents as being multifunctional or capable of synergizing multiple key mechanisms driving the breakdown of biomass into valuable chemical precursors. Molecular simulations reveal that lignin globules expand in THF-water, an excellent "theta" solvent, dissociating both from themselves and from cellulose. The expansion of the lignin molecules in THF-water further exposes inter-unit linkages, rendering them susceptible to acid-catalyzed fragmentation by cleavage of aryl-ether bonds. Nanoscale infrared sensors confirm co-solvent mediated molecular rearrangement of lignin in the cell wall of micron-thick hardwood slices and track the disappearance of lignin. At bulk scale, dilute acid pretreatment of biomass in a co-solvent mixture liberates hemicellulose and depolymerized lignin from cellulose, allowing unfettered access of cellulolytic enzymes that sustain high rates of cellulose hydrolysis to glucose without enzyme deactivation. Through this multi-scale analysis, synergistic mechanisms can be identified for other multifunctional co-solvents portending a paradigm shift towards first principles design of future biomass deconstruction methods in order to realize lower cost fuels.
Fundamental mechanisms for molecular energy conversion and chemical reactions at surfaces

The dream of theoretical surface chemistry is to predict the outcome of reactions in order to find the ideal catalyst for a certain application. Having a working ab initio theory in hand would not only enable these predictions but also provide insights into the mechanisms of surface reactions. The development of theoretical models can be assisted by experimental studies providing benchmark data. Though for some reactions a quantitative agreement between experimental observations and theoretical calculations has been achieved, theoretical surface chemistry is in general still far away from gaining predictive power. Here we review recent experimental developments towards the understanding of surface reactions. It is demonstrated how quantum-state resolved scattering experiments on reactive and nonreactive systems can be used to test front-running theoretical approaches. Two challenges for describing dynamics at surfaces are addressed: nonadiabaticity in diatomic molecule surface scattering and the increasing system size when observing and describing the dynamics of polyatomic molecules at surfaces. Finally recent experimental studies on reactive systems are presented. It is shown how elementary steps in a complex surface reaction can be revealed experimentally.
Facial muscle reanimation by transcutaneous electrical stimulation for peripheral facial nerve palsy

Abstract Reanimation of paralysed facial muscles by electrical stimulation has been studied extensively in animal models, but human studies in this field are largely lacking. Twenty-four subjects with a peripheral facial nerve palsy with a median duration of three years were enrolled. We studied activations of four facial muscles with electrical stimulation using surface electrodes. In subjects whose voluntary movement was severely impaired or completely absent, the electrical stimulation produced a movement that was greater in amplitude compared with the voluntary effort in 10 out of 18 subjects in the frontalis muscle, in 5 out of 14 subjects in the zygomaticus major muscle, and in 3 out of 8 subjects in the orbicularis oris muscle. The electrical stimulation produced a stronger blink in 8 subjects out of 22 compared with their spontaneous blinks. The stimulation could produce a better movement even in cases where the muscles were clinically completely paretic, sometimes also in palsies that were several years old, provided that the muscle was not totally denervated. Restoring the function of paralysed facial muscles by electrical stimulation has potential as a therapeutic option in cases where the muscle is clinically paretic but has reinnervation.
Node Labeling Schemes in XML Query Optimization: A Survey and Trends

Abstract With the rapid emergence of XML as a data exchange and data transfer medium over the Web, querying XML data has become a major concern. Labeling schemes have been developed to optimize query retrieval, since they provide a quick way to determine the type of relationships that are present among the nodes. In this paper, we analyze how each approach works, as well as its advantages and disadvantages. In addition, we discuss some of the current trends in labeling methods, which indicate a clear shift towards hybrid approaches. Hybrid systems open the possibility of balancing one technology’s weakness with another technology’s strengths.
State feedback control synthesis for networked control systems with packet dropout

This paper is concerned with the problem of H∞ controller design for networked control systems (NCSs) with time delay and packet dropout. A combined switching and parameter uncertainty‐based method is proposed to deal with time‐varying delay. The proposed method can avoid the high computational complexity of the delay switching‐based method and introduce less conservatism than the parameter uncertainty‐based method. An active varying sampling period method is proposed to make full use of network bandwidth, and a multi‐objective optimization methodology in terms of linear matrix inequalities is used to deal with H∞ controller design for NCSs with active varying sampling period. The simulation results illustrate the effectiveness of the proposed active varying sampling period method and the less conservatism of the combined switching and parameter uncertainty‐based method. Copyright © 2009 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society