julilili42/papers huggingface dataset:
A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data
2006-11-01

The subphylum Ustilaginomycotina comprises about 1500 species of basidiomycetous plant parasites. They are usually dimorphic, producing a saprobic haploid yeast phase and a parasitic dikaryotic hyphal phase. With only a few exceptions they occur on angiosperms and are found mainly on members of the Poaceae and Cyperaceae. Molecular methods recently have shown that anamorphic species such as members of Malassezia or Tilletiopsis should be included in this group. Here we present the most recent consensus as to the phylogeny of this group and discuss its relevant characteristics. Our morphological, ultrastructural and molecular phylogenetic data point to the existence of three lines of Ustilaginomycotina: Entorrhizomycetes, Ustilaginomycetes and Exobasidiomycetes. Entorrhizomycetes is represented by Entorrhizales, a small group of unusual teliosporic root parasites on Juncaceae and Cyperaceae. Ustilaginomycetes, to which the majority of Ustilaginomycotina belong, is a teliosporic and gastroid group characterized by the presence of enlarged interaction zones. Ustilaginomycetes is dichotomous, consisting of predominantly holobasidiate Urocystales and predominantly phragmobasidiate Ustilaginales. Exobasidiomycetes forms local interaction zones. This group is predominantly holobasidiate and consists of teliosporic Doassansiales, Entylomatales, Georgefischeriales and Tilletiales, nonteliosporic Ceraceosorales, Exobasidiales and Microstromatales, as well as the anamorphic Malasseziales. Entorrhizomycetes, Exobasidiomycetes and Ceraceosorales are proposed as new taxa, and the description of Ustilaginomycetes is emended.
The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods
2006-11-01

We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that clade. Phylogenetic analyses support monophyly of all genera except Sistotrema, which was highly polyphyletic. Strongly supported monophyletic groups were: (i) Cantharellus-Craterellus, Hydnum, and the Sistotrema confluens group; (ii) Clavulina-Membranomyces and the S. brinkmannii-oblongisporum group, with Multiclavula being possibly sister of that clade; (iii) the Sistotrema eximum-octosporum group; (iv) Sistotrema adnatum and S. coronilla. Positions of Sistotrema raduloides and S. athelioides were unresolved, as were basal relationships. Botryobasidium was well supported as the sister taxon of all the above taxa, while Ceratobasidiaceae was the most basal lineage. The relationship between Tulasnella and members of the cantharelloid clade will require further scrutiny, although there is cumulative evidence that they are probably sister groups. The rates of molecular evolution of both the large and small nuclear ribosomal RNA genes (nuc-rDNA) are much higher in Cantharellus, Craterellus and Tulasnella than in the other cantharelloid taxa, and analyses of nuc-rDNA sequences strongly placed Tulasnella close to Cantharellus-Craterellus. In contrast analyses with RPB2 and mtSSU sequences placed Tulasnella at the base of the cantharelloid clade. Our attempt to reconstruct a "supertree" from tree topologies resulting from separate analyses that avoided phylogenetic reconstruction problems associated with missing data and/or unalignable sequences proved unsuccessful.
Assembling the Fungal Tree of Life: constructing the Structural and Biochemical Database
2006-11-01

A major goal of the Assembling the Fungal Tree of Life project is to create a searchable database <http://aftol.umn.edu> of selected ultrastructural and biochemical characters from published and new data for use in phylogenetic and other analyses. While developing this database such issues as evaluating specimen fixation quality in published micrographs, organizing data to accommodate characters that were dependent on location and developmental stage, and requiring accountability of data contributors were addressed. Character states for three traits, septal pore apparatus, nuclear division and spindle pole body cycle, are illustrated, and character states are resolved with maximum parsimony and plotted on a summary cladogram of known phylogenetic relationships of the Fungi. The analysis illustrates the inherent phylogenetic signal of these characters, the paucity of comparable characters and character states in subcellular studies and the challenges in establishing a comprehensive structural and biochemical database of the Fungi.
An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences
2006-11-01

In this study we provide a phylogenetically based introduction to the classes and orders of Pucciniomycotina (= Urediniomycetes), one of three subphyla of Basidiomycota. More than 8000 species of Pucciniomycotina have been described including putative saprotrophs and parasites of plants, animals and fungi. The overwhelming majority of these (~90%) belong to a single order of obligate plant pathogens, the Pucciniales (= Uredinales), or rust fungi. We have assembled a dataset of previously published and newly generated sequence data from two nuclear rDNA genes (large subunit and small subunit) including exemplars from all known major groups in order to test hypotheses about evolutionary relationships among the Pucciniomycotina. The utility of combining nuc-lsu sequences spanning the entire D1–D3 region with complete nuc-ssu sequences for resolution and support of nodes is discussed. Our study confirms Pucciniomycotina as a monophyletic group of Basidiomycota. In total our results support eight major clades ranked as classes (Agaricostilbomycetes, Atractiellomycetes, Classiculomycetes, Cryptomycocolacomycetes, Cystobasidiomycetes, Microbotryomycetes, Mixiomycetes and Pucciniomycetes) and 18 orders.
The Mean Square Error of Prediction in the Chain Ladder Reserving Method (Mack and Murphy Revisited)
2006-11-01

We revisit the famous Mack formula [2], which gives an estimate for the mean square error of prediction MSEP of the chain ladder claims reserving method: We define a time series model for the chain ladder method. In this time series framework we give an approach for the estimation of the conditional MSEP. It turns out that our approach leads to results that differ from the Mack formula. But we also see that our derivation leads to the same formulas for the MSEP estimate as the ones given in Murphy [4]. We discuss the differences and similarities of these derivations.
Inhibition of Human 5-Lipoxygenase and Anti-Neoplastic Effects by 2-Amino-1,4-Benzoquinones
2006-11-01

We have recently presented the synthesis of 2-amino-1,4-benzoquinones by nuclear amination of p-hydroquinones with primary aromatic amines using fungal laccases as catalysts. In the present report, a series of selected 2-amino-1,4-benzoquinones was tested for biological activities, such as inhibition of human 5-lipoxygenase and anti-proliferative/anti-neoplastic effects. Compound 9 (2-[4'-(iso-propylphenyl)-amino]-5,6-dimethyl-1,4-benzoquinone) was identified as the most potent aminoquinone derivative, suppressing 5-lipoxygenase in intact human polymorphonuclear leukocytes as well as in crude enzyme preparations in the low micromolar range (IC50 = 6 microM). Structure-activity relationships are discussed. Of interest, the 5-lipoxygenase inhibitory properties of 2-amino-1,4-benzoquinones in intact cells correlated to the anti-neoplastic activities of the compounds in breast and urinary bladder cancer cell lines. Based on these features, bioactive 2-amino-1,4-benzoquinones may possess potential for the pharmacological treatment of diseases associated with elevated 5-lipoxygenase activity, in particular certain types of cancer.
Flexible Flow Aggregation for Adaptive Network Monitoring
2006-11-01

Network monitoring is a major building block for many domains in communication networks. Besides typical accounting mechanisms and the emerging area of charging in next generation networks, especially network security solutions rely on efficient and optimized monitoring. Network monitoring in high-speed networks is usually based on flow accounting and aggregation techniques represent a necessary enhancement in order to cope with increasing amounts of monitoring data that accrue with the ever-growing network capacities. In this paper, we propose a flexible flow aggregation mechanism that can be directly employed on a monitoring probe to reduce the memory and processing demands. Alternatively, it can work as a concentrator that collects flow data from multiple monitoring probes, combines and aggregates them and forwards the results to an analyzer. We verified and evaluated the aggregation mechanism by integrating it into our monitoring probe Vermont. Our approach opens new prospects for high-speed network monitoring and allows coping with special situations that cannot be treated satisfyingly by traditional flow accounting, such as distributed denial-of-service attacks causing very high numbers of flows. Aggregated flow data are an easy-to-handle form of packet information especially for anomaly detection and accounting issues
Temporal and spatial enumeration processes in the primate parietal cortex
2006-11-01

Humans and animals can nonverbally enumerate visual items across time in a sequence or rapidly estimate the set size of spatial dot patterns at a single glance. We found that temporal and spatial enumeration processes engaged different populations of neurons in the intraparietal sulcus of behaving monkeys. Once the enumeration process was completed, however, another neuronal population represented the cardinality of a set irrespective of whether it had been cued in a spatial layout or across time. These data suggest distinct neural processing stages for different numerical formats, but also a final convergence of the segregated information to form most abstract quantity representations.
Voices of the dead: Complex nonlinear vocal signals from the larynx of an ultrasonic frog
2006-11-01

Most anurans are highly vocal but their vocalizations are stereotyped and simple with limited repertoire sizes compared to other vocal vertebrates, due presumably to the limited mechanisms for fine vocal motor control. We recently reported that the call of the concave-eared torrent frog (Amolops tormotus) is an exception in its seemingly endless variety, musical warbling quality, extension of call frequency into the ultrasonic range, and the prominence of nonlinear features such as period doubling. We now show that the major spectral features of its calls, responsible for this frog’s vocal diversity, can be generated by forcing pressurized air through the larynx of euthanized males. Laryngeal specializations for ultrasound appear to include very thin portions of the medial vocal ligaments and the reverse sexual size dimorphism of the larynx being smaller in males than in females. The intricate morphology of the vocal cords, which changes along their length, suggests that nonlinear phenomena likely arise from complex nonlinear oscillatory regimes of separate elastically coupled masses. Amolops is thus the first amphibian for which the intrinsic nonlinear dynamics of its larynx, a relatively simple and expedient mechanism, can account for the species call complexity, without invoking sophisticated neuromuscular control.
A Magnetic Study of a Polluted Soil Profile at the Shijingshan Industrial Area, Western Beijing, China
2006-11-01

A soil profile of 74 cm length was sampled in the hillside close to Beijing Muslim's cemetery, which is located in the Yingshan Forest Park near the Shijingshan industrial area. Coal-fired power plants, a steel mill, and a cement factory are located close to the sampling site. Gray-black pollutants can be found within the uppermost part of the soil. Magnetic measurements, grain size and geochemical analysis, as well as multivariate statistics were performed. Magnetic proxies show similar trends compared to heavy metal elements with higher concentrations at the top and lower concentrations in the lower part. The anthropogenic dust input from industrial activity is the predominant cause for strong magnetic signals in the uppermost soil horizon (0~3 cm). The main magnetic component is magnetite contained in the grain size fractions of 4~16μm and 16~32μm. These pollutants are observed up to about 10 cm depth. Below 10 cm, there is little pollution in soil with lowest concentration of magnetic minerals and heavy metals comparable to natural background values. Multivariate statistics and fuzzy C-means cluster analysis show positive correlation of χ, ARM, SIRM and Mn, Cu, Fe, Pb, Zn, Al, Sr. Based on the results, it can be concluded that magnetic parameters can be used as a sensitive indicator for screening heavy metal pollution.
The curtain is drawn for both natalizumab and fingolimod (FTY720): a new era of multiple sclerosis therapy has arrived
2006-11-01

A new era of treatment in multiple sclerosis (MS) has arrived. Novel drugs target the migration of T lymphocytes to the CNS in MS. With the introduction of natalizumab (TysabriTM, Biogen Idec), a n...
Characterization and operation of a mechanically actuated silicon microgripper
2006-11-01

Since the manipulation of biological objects is usually performed in a life-sustaining environment, electrical fields or thermal gradients through the liquid may cause perturbations. The authors present a microgripper fabricated in silicon by a combination of bulk and surface micromachining processes that exhibits several advantages compared to previous reports. In order to avoid any possible perturbation caused by electrical fields, their microgripper is mechanically actuated. The complete system including the microgripper, a piezoactuator, and a nanomanipulator is described in detail together with manipulation of micrometer sized glass spheres.
Contactless capturing of particles in liquid using pulsed alternating dielectrophoresis
2006-11-01

Dielectrophoresis is an effective method for manipulation of particles in a medium, which can be achieved by applying electrical potentials to appropriately arranged electrodes. In the case of positive dielectrophoresis, the particles will move to regions of strong electric field and be captured at the edge or the surface of the electrodes, usually. The drawback thereby is that the particles may attach to the electrodes, leading to unwanted side effects. Negative dielectrophoresis moves them away from high field regions. In this article, the authors present a new method for contactless capturing of particles by using pulsed alternating dielectrophoresis. A signal sequence consisting of two pulsed ac voltages of different frequencies is applied to the electrodes. Each of them generates either positive or negative dielectrophoresis, respectively. With appropriate settings of dwell times and amplitudes, the particles are attracted toward the electrodes without attaching to them. Furthermore, the average distance from the electrodes can be tuned. Their experiments show that latex beads could be kept at a distance of up to about 20μm from the electrodes.
Reconstruction of bat sonar beams using a multichannel microphone array
2006-11-01

We reconstruct the sonar beams emitted subsequently by flying bats from recordings of a two-dimensional microphone array. Based on the bats’ position in space, which can be accessed through a infrared 3D-video system, and the simultaneous recordings of 16 small microphones, the sonar beams emitted by the bats and the sonar footprints on arbitrary planes can be estimated. For the interpolation of a continuous sonar beam at different frequency bands, directional frequency responses, atmospheric and geometric attenuation, and different lag times are taken into account for each microphone. Mean and maximum call intensities can be analyzed and various analysis parameters can be adjusted, different visualizations are available, and numerical data are exported. The system provides access to estimations of the maximum intensity of each call in front of the bat, beam width, shape, and intensity for arbitrary frequency bands, the aiming of the beam, and the bat’s scanning behavior on its flight path.
Depositing archived paraffin tissue core biopsy specimens in paraffin tissue microarrays using a paraffin tissue punch modified with a countersink: Figure 1
2006-11-01

Paraffin tissue microarrays (PTMAs) introduced by Kononen et al in 1998 have become a widely used technique in routine pathology and even more so in research. Kononen used a tissue puncher/arrayer (Beecher Instruments, Sun Prairie, WI, USA) to take paraffin tissue core biopsy specimens (PTCBs) of 0.6–2 mm in diameter from routine paraffin tissue blocks and transfer them to another paraffin block with up to 1000 holes. As pointed out by Mengel et al , however, it is not possible to use the Kononen/Beecher system to construct PTMAs out of archived PTCBs. To overcome this drawback in the extremely popular Beecher system, the paraffin tissue punch was modified by incorporating a conical 4 mm deep countersink. This countersink was milled with a conical precision cutter that can be bought in an ordinary hardware store (cost &lt;US$5). The countersink facilitates the insertion of an archived PTCB into the paraffin tissue punch and enables the construction of PTMAs with previously archived PTCBs using the widely distributed Beecher system. Moreover, this paraffin tissue punch can be used for other systems to create PTMAs, such as the low-budget systems designed by Vogel.
Cerco: Supporting Range Queries with a Hierarchically Structured Peer-to-Peer System
2006-11-01

Structured peer-to-peer systems are designed for a highly scalable, self organizing, and efficient lookup for data. The key space of the so-called distributed hash tables (DHTs) is partitioned and each partition with its keys and values is assigned to a node in the DHT. For data retrieval however, the very nature of hash tables allows only exact pattern matches. We propose Cerco, a simple solution for the problem of range queries by employing a hierarchically structured P2P approach based on the principles of distributed hash tables. We show that a dynamic hierarchy of DHTs with on-demand classification of items can positively influence the response time of queries while maintaining lookup correctness
Synthesis of First Tetrathiafulvalene-Carbohydrate Derivatives
2006-11-01

In this communication a convenient and novel method for the synthesis of tetrathiafulvalenecarbohydrate (TTF) derivatives from anhydro triflyl-, iodo- and bromo-sugars is described. Keywords: Synthesis, tetrathiafulvalene-carbohydrate (TTF), anhydo triflyl-, iodo-, bromo-, sugars
The sonar beam of big brown bats (Eptesicus fuscus) during landing
2006-11-01

The parameters signal duration, pulse interval, and frequency have previously been used to describe the approach behavior of landing bats. An array with 16 microphones was used to investigate additional parameters during the approach flight of landing big brown bats (Eptesicus fuscus). For each signal emitted the position of the landing bat in relation to the microphone array was determined using a 3-D video system, and the width, maximum intensity, and aiming direction of the sonar beam were calculated. The approach to the landing site begins at a distance of about 1.4 m when the bats pick up the landing site with their sonar beam. This focusing on the landing site is indicated by a clear decrease of the deviation between beam aiming and direction to the landing position. The maximum intensity of the sonar beam is reduced by about 6 dB per half distance during the last 2 m of the approach, which indicates a gain control mechanism. The width of the sonar beam remains constant throughout the whole approach.
Triazole-annulated phthalocyanines and benzoporphyrazines
2006-11-01

The application of mono-triazole-annulated phthalocyanine and benzoporphyrazine complexes for the functional unsymmetrical modification of the macrocycle's periphery is discussed. The peculiarities of the synthesis of some metal complexes with aryloxy-substituted mono-triazole-annulated Pc are described. Alkylation by ω-alkenylbromide of the triazole ring in accordingly prepared novel mono-triazole-annulated phthalocyaninato nickel, as well as in mono-benzotriazole-annulated porphyrazinato zinc, is studied. The terminal double bond in the formed derivatives could be successfully converted into acetylsulfanyl function only in the case of phthalocyaninato nickel complex due to the instability of porphyrazinato zinc under the reaction conditions.
Influence of the Two-Component System SaeRS on Global Gene Expression in Two Different Staphylococcus aureus Strains
2006-11-02

ABSTRACT The two-component system SaeRS consisting of the histidin kinase SaeS and the response regulator SaeR is known to act on virulence gene expression in Staphylococcus aureus . In order to get a more comprehensive picture on SaeR-regulated genes, we studied the contribution of the two-component system on global gene expression by using both the proteomic and transcriptomic approach. Altogether, a loss of SaeRS resulted in a decreased amount of at least 17 extracellular proteins and two cell surface-associated proteins, among them several important virulence factors such as HlgA, HlgB, HlgC, LukF, and LukM. SaeRS activates the expression of these genes at the transcriptional level. The amount of the five proteins Aur, SspA, SsaA, Plc, and GlpQ was negatively influenced by SaeRS. However, the transcription of the corresponding genes was not affected by the two-component system. SaeRS had also no measurable influence on the transcription of the regulatory genes agr , sarA , arlRS , and sigB that contribute to the regulation of SaeRS-dependent virulence factors identified in this investigation. Our results clearly show that SaeRS is strongly involved in the tight temporal control of virulence factor expression in S. aureus . Its precise role within the regulatory network remains to be determined.
Neural Internet: Web Surfing with Brain Potentials for the Completely Paralyzed
2006-11-02

Neural Internet is a new technological advancement in brain-computer interface research, which enables locked-in patients to operate a Web browser directly with their brain potentials. Neural Internet was successfully tested with a locked-in patient diagnosed with amyotrophic lateral sclerosis rendering him the first paralyzed person to surf the Internet solely by regulating his electrical brain activity. The functioning of Neural Internet and its clinical implications for motor-impaired patients are highlighted.
‘To repair or not to repair – no longer a question’: repair of mitochondrial DNA shielding against age and cancer
2006-11-02

Abstract: The role of mitochondria in energy production and apoptosis is well known. The role of mitochondria and particularly the role of the mitochondria's own genome, mitochondrial (mt) DNA, in the process of ageing were postulated decades ago. However, this was discussed, debated and more or less disposed of. Recent data from elegant mouse models now confirm that mutations of mtDNA do indeed play a central and pivotal role in the ageing process. Newer reports also indicate a possible role of mtDNA mutations in the carcinogenesis of several organs. But is damaged mtDNA repaired, or is it simply degraded and discarded? This question appears to be answered now. According to recent data, mitochondria possess functional repair mechanisms such as base excision repair, double‐strand break repair and mismatch repair, yet nucleotide excision repair has so far not been detected.