Miracle-dz/UniFAR-FTUs huggingface dataset:
Endosymbionts of Siboglinum fiordicum and the Phylogeny of Bacterial Endosymbionts in Siboglinidae (Annelida)

Siboglinid worms are a group of gutless marine annelids that are nutritionally dependent upon endosymbiotic bacteria. Four major groups of siboglinids are known—vestimentiferans, moniliferans, Osedax spp. and frenulates. Although endosymbionts of vestimentiferans and Osedax spp. have been previously characterized, little is currently known about endosymbiotic bacteria associated with frenulate and moniliferan siboglinids. This is particularly surprising given that frenulates are the most diverse and widely distributed group of siboglinids. Here, we molecularly characterize endosymbiotic bacteria associated with the frenulate siboglinid Siboglinum fiordicum by using 16S rDNA ribotyping in concert with laser-capture microdissection (LCM). Phylogenetic analysis indicates that at least three major clades of endosymbiotic γ-proteobacteria associate with siboglinid annelids, with each clade corresponding to a major siboglinid group. S. fiordicum endosymbionts are a group of γ–proteobacteria that are divergent from bacteria associated with vestimentiferan or Osedax hosts. Interestingly, symbionts of S. fiordicum, from Norway, are most closely related to symbionts of the frenulate Oligobrachia mashikoi from Japan, suggesting that symbionts of frenulates may share common evolutionary history or metabolic features.
Project management with high complexity and uncertainty in a government organization: A case study of the Sao Paulo Tax Invoice system development

This case study analyzes the development of an incentive system to avoid fiscal evasion. It is named Sao Paulo Tax Invoice. It is an innovative way to use Information Technology (IT) to enforce tax collect in the retail sector. It was started in 2007 by the State of Sao Paulo Treasury. The government stimulates product buyers to ask for a tax receipt, at the checkout on retail stores, by returning to them a percentage of the tax paid by the store. Every six months the treasury calculates a tax devolution and consumers can register online and choose to receive the money directly on a bank account or through a state's tax deduction. Another incentive is an automatic lottery draw system that distribute money prizes and rewards to assiduous users. These became the motto of the marketing campaign, “the more you ask, the more you gain”, with massive advertising, including television commercials, resulting in more than 17 million users registered. The objective of this paper is to address this initiative origin and its development process. Our results show that due to the political importance and many uncertainties involved, the project leader adopted a non conventional project management approach. Studies suggest there was a 22% increase in fiscal revenue in first years, indicating the system's success.
Review Lecture - Replication of DNA in the chromosomes of eukaryotes

The evidence that each chromatid of a eukaryotic organism contains only one DNA double helix comes from a variety of observations. It begins with the autoradiographic demonstration by J. H. Taylor that tritiated thymidine, incorporated into chromosomes during one round of DNA synthesis, is present in both chromatids at the first division after labelling, but in only one chromatid after a further round of DNA synthesis accomplished in the absence of label. Further evidence comes from those experiments which demonstrate that when two sister chromatids break and fuse one with the other, each chromatid behaves as though it contained two chains of opposite polarity, fusion between chains being restricted to those of like polarity. J. G. Gall’s study of the kinetics of digestion of lampbrush chromosomes by pancreatic DNase also supports the view that each chromatid contains only two polynucleotide chains which are cleaved by this enzyme independently of one another; while O. L. Miller’s observations on the dimensions of the fibres remaining after lampbrush chromosomes have been digested by trypsin only allow for there being two polynucleotide chains per chromatid. By means of the technique of DNA fibre autoradiography devised by J. A. Huberman and A. D. Riggs, the units involved in replicating the chromosomal DNA of somatic cells of Xenopus have been compared with those of Triturus. Both these organisms have initiation points for DNA replication that are arranged in tandem, and from each initiation point replication proceeds in opposite directions at divergent forks. The intervals between initiation points in Xenopus range from about 20 to 125 µm apart, whereas those of Triturus are much more widely separated. At 25 °C replication of DNA in Xenopus somatic cells proceeds at 9 µm per hour one-way at each fork, whereas the corresponding rate in Triturus is 20 µm per hour. Triturus somatic cells take about 4 times longer than comparable cells of Xenopus to replicate their DNA. The Triturus genome contains about 10 times as much DNA as the Xenopus genome, and comparison of the replication process in these two organisms indirectly adds weight to the view that the Triturus genome is 10 times longer than that of Xenopus, rather than that it contains 10 times as many DNA double helices per chromatid. DNA fibre autoradiography has also been used to study replication in Triturus spermato-cytes. The round of DNA synthesis just before meiosis in Triturus is an exceptionally long-drawn-out process, taking 9 to 10 days for completion at 16 °C. This lengthy S-phase is not occasioned by abnormally slow replication, the rate being 12 µm per hour one-way at 18 °C, nor is it the result of an exceptional staggering of replication starts. Instead it appears to be correlated with a gross reduction in the number of initiation points for replication. i.e. with an increase in the lengths of the replicating units. A rough calculation suggests that each meiotic chromomere may correspond to a unit of replication during the pre-meiotic S-phase.
Nuclear Receptor Nr4a2 Promotes Alternative Polarization of Macrophages and Confers Protection in Sepsis*♦

Background: An understanding of the role of Nr4a2 in inflammation is needed. Results: Nr4a2 is a transcription factor that induces expression of M2 characteristic genes, and adoptive transfer of macrophages overexpressing Nr4a2 gives protection against septic mortality. Conclusion: Our data impart a new role for Nr4a2 in skewing macrophage plasticity to M2 type. Significance: Therapeutic intervention of Nr4a2 may provide a cure for inflammatory diseases. The orphan nuclear receptor Nr4a2 is known to modulate both inflammatory and metabolic processes, but the mechanism by which it regulates innate inflammatory homeostasis has not been adequately addressed. This study shows that exposure to ligands for Toll-like receptors (TLRs) robustly induces Nr4a2 and that this induction is tightly regulated by the PI3K-Akt signaling axis. Interestingly, exogenous expression of Nr4a2 in macrophages leads to their alternative phenotype with induction of genes that are prototypical M2 markers. Moreover, Nr4a2 transcriptionally activates arginase 1 expression by directly binding to its promoter. Adoptive transfer experiments revealed that increased survival of animals in endotoxin-induced sepsis is Nr4a2-dependent. Thus our data identify a previously unknown role for Nr4a2 in the regulation of macrophage polarization.
Benchmark datasets for 3 D MALDI-and DESI-imaging mass spectrometry

Background: Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms. Findings: High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D desorption electrospray ionization (DESI) imaging MS data were collected from a human colorectal adenocarcinoma. Conclusions: With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets.
Experimental studies on intermolecular, hydrodynamic and capillary interactions at the nanoscale

Las interacciones intermoleculares, hidrodinamicas y capilares en la nanoescala estan de actualidad debido a su importancia en las aplicaciones biologicas y biomedicas. Esta tesis, de caracter experimental, pero estrechamente vinculada a las interpretaciones teoricas de los fenomenos fisicos que intervienen en estas interacciones, se ha desarrollado principalmente en torno a dos objetivos: estudiar el papel de las interacciones capilares y la histeresis de adhesion en la Microscopia de Fuerzas Atomicas operado en aire, y desarrollar una nueva tecnica experimental capaz de detectar interacciones moleculares entre nanoparticulas magneticas funcionalizadas y biomoleculas en medios biologicos. Uno de los resultados mas relevantes de esta tesis es que la adhesion capilar entre dos superficies hidrofilas depende en gran medida de la geometria en la nanoescala. Particularmente sorprendente fue el descubrimiento de que la adhesion capilar incluso puede disminuir con la humedad. Se han realizado trabajos para estudiar el efecto de la histeresis de adhesion en el modo dinamico de la Microscopia de Fuerzas Atomicas, con el fin de investigar la relacion entre la potencia disipada obtenida experimentalmente y propiedades fisicoquimicas de la muestra. Por otro lado, en vista de una futura aplicacion en el campo de biosensores de reconocimiento molecular basados en nanoparticulas, se ha implementado un montaje experimental para detectar la birrefringencia magnetica transitoria en una suspension de nanoparticulas magneticas mediante la aplicacion de un campo magnetico pulsado. Esta tecnica magneto-optica permite utilizar nanoparticulas como sondas para detectar el reconocimiento molecular in situ en tejidos o celulas. Se demuestra que los diametros hidrodinamicos de pequenos agregados anisotropos se pueden determinar in situ en geles de agarosa - un sistema modelo compatible con la separacion por electroforesis. Ademas, la tecnica se ha aplicado para detectar el reconocimiento molecular de Concanavalina A por nanoparticulas superparamagneticas funcionalizadas con glucosa.
Inhibiting Alternative Pathway Complement Activation by Targeting the Factor D Exosite*

Background: Anti-factor D antibody blocks a rate-limiting step in the alternative complement pathway. Results: The structure of anti-factor D in complex with factor D provides the molecular basis of complement inhibition. Conclusion: Anti-factor D binds to the factor D exosite and inhibits alternative pathway complement activation. Significance: Targeting the exosite on proteases could have great potential for antibody therapies. By virtue of its amplifying property, the alternative complement pathway has been implicated in a number of inflammatory diseases and constitutes an attractive therapeutic target. An anti-factor D Fab fragment (AFD) was generated to inhibit the alternative complement pathway in advanced dry age-related macular degeneration. AFD potently prevented factor D (FD)-mediated proteolytic activation of its macromolecular substrate C3bB, but not proteolysis of a small synthetic substrate, indicating that AFD did not block access of the substrate to the catalytic site. The crystal structures of AFD in complex with human and cynomolgus FD (at 2.4 and 2.3 Å, respectively) revealed the molecular details of the inhibitory mechanism. The structures show that the AFD-binding site includes surface loops of FD that form part of the FD exosite. Thus, AFD inhibits FD proteolytic function by interfering with macromolecular substrate access rather than by inhibiting FD catalysis, providing the molecular basis of AFD-mediated inhibition of a rate-limiting step in the alternative complement pathway.
Erbium in crystal silicon: Optical activation, excitation, and concentration limits

The optical activation, excitation, and concentration limits of erbium in crystal Si are studied. Preamorphized surface layers of Czochralski‐grown (Cz) Si(100), containing 1.7×1018 O/cm3, were implanted with 250 keV Er at fluences in the range 8×1011–8×1014 cm−2. After thermal solid‐phase epitaxy of the Er‐doped amorphous layers at 600 °C, Er is trapped in the crystal at concentrations ranging from 3×1016 to 7×1019 Er/cm3, as measured by secondary‐ion‐mass spectrometry. Photoluminescence spectra taken at 77 K show the characteristic Er3+ intra‐4f luminescence at 1.54 μm. Photoluminescence excitation spectroscopy shows that Er is excited through a photocarrier‐mediated process. Rapid thermal annealing at 1000 °C for 15 s increases the luminescence intensity, mainly due to an increase in minority‐carrier lifetime, which enhances the excitation efficiency. Luminescent Er forms clusters with oxygen: the maximum Er concentration that can be optically activated is determined by the O content, and is (3±1)×1017.
Investigating the content and form of referring expressions in Mandarin: introducing the Mtuna corpus

East Asian languages are thought to handle reference differently from languages such as English, particularly in terms of the marking of definiteness and number. We present the first Data-Text corpus for Referring Expressions in Mandarin, and we use this corpus to test some initial hypotheses inspired by the theoretical linguistics literature. Our findings suggest that function words deserve more attention in Referring Expressions Generation than they have so far received, and they have a bearing on the debate about whether different languages make different trade-offs between clarity and brevity.
Fraud Detection in Comparison-Shopping Services: Patterns and Anomalies in User Click Behaviors

This paper deals with a novel, interesting problem of detecting frauds in comparison-shopping services (CSS). In CSS, there exist frauds who perform excessive clicks on a target item. They aim at making the item look very popular and subsequently ranked high in the search and recommendation results. As a result, frauds may distort the quality of recommendations and searches. We propose an approach of detecting such frauds by analyzing click behaviors of users in CSS. We evaluate the effectiveness of the proposed approach on a real-world clickstream dataset. key words: fraud detection, comparison-shopping services, user behavior analysis
Identification of longitudinal acoustic modes guided in the core region of a single-mode optical fiber by Brillouin gain spectra measurements.

Several resonance peaks owing to an interaction between light-wave and guided modes of longitudinal acoustic waves are observed in the Brillouin gain spectra for a single-mode fiber with a GeO2-doped core and pure silica cladding. Brillouin gain spectra measurements are carried out at 1286- and 1550-nm wavelengths. Longitudinal acoustic modes guided in the GeO2-doped core region are identified by applying the analysis of leaky modes in a fiber acoustic waveguide.
Evolution in the Arctic: a phylogeographic analysis of the circumarctic plant, Saxifraga oppositifolia (Purple saxifrage)

Summary • A survey of chloroplast DNA variation in the circumarctic-alpine plant, Saxifraga oppositifolia, has resolved two highly divergent cpDNA lineages with geographically widespread and mainly allopatric distributions that are largely concordant with those of two subspecies, that is, subspp. oppositifolia and glandulisepala. These subspecies differ for a single morphological trait and hence level of morphological divergence does not equate to molecular divergence within the species. • The two cpDNA lineages were estimated to have diverged from their most recent common ancestor 5.37–3.76 Ma, that is, during the early to mid-Pliocene. • A nested clade analysis was conducted in an attempt to determine how past episodes of range fragmentation, range expansion and long distance dispersal may have influenced the geographical distribution of cpDNA haplotypes. • In Alaska – a known refugium for the species during the last ice-age – high levels of cpDNA diversity may be partly explained by divergence between populations that were isolated in different ice-free regions. It remains to be established whether the two subspecies of S. oppositifolia exhibit some form of reproductive isolation from each other under conditions of sympatry.
Effect of the Culture Nutrients on the Biomass an Lipid Productivities of Microalgae Dunaliella Tertiolecta

Effect of the Culture Nutrients on the Biomass and Lipid Productivities of Microalgae Dunaliella tertiolecta Teresa M. Mata*, Ricardo Almeida, Nidia S. Caetano LEPAE – Laboratory for Process, Environmental and Energy Engineering, Faculty of Engineering, University of Porto (FEUP), R. Dr. Roberto Frias S/N, 4200-465 Porto, Portugal Department of Chemical Engineering, School of Engineering (ISEP), Polytechnic Institute of Porto (IPP), R. Dr. Antonio Bernardino de Almeida S/N, 4200-072 Porto, Portugal * tmata@fe.up. pt
A communication architecture tailored for analog VLSI artificial neural networks: intrinsic performance and limitations

An architecture for interchip communication among analog VLSI neural networks is proposed. Activity is encoded in a neuron's pulse emission frequency. Information is transmitted through the non-arbitered, asynchronous access of pulses to a common bus. The impact of collisions when the bus is accessed by more than one user is investigated. The information-carrying capability is assessed and the trade-off between accuracy of the transmitted information and attainable dynamic range is brought out in terms of simple global parameters that characterize the application. It is found that the proposed architecture is well suited for the kind of communication requirements associated to neural computation systems. A coding scheme aimed at pushing the system towards its theoretical performance is also presented and evaluated.
Studies on the enzymatic reduction of C-nitroso compounds. V. Molecular properties of porcine heart C-nitrosoreductase and identity of this enzyme with NAD(P)H dehydrogenase.

NAD(P)H-dependent C-nitrosoreductase of porcine heart cytosol was purified 12,000-fold in the presence of NADH with an overall yield of 2.2%. The purification procedure included ammonium sulfate fractionation, gel filtration with Sephadex G-100, ion-exchange chromatography on DEAE-Sephadex A-50, hydrophobic chromatography on Octyl-Sepharose CL-4B, and gel filtration with Sephadex G-200. The purity of the preparation was approximately 90% and the molecular weight of the enzyme estimated by gel filtration was about 60,000. The purified enzyme was composed of two molecular forms, nitrosoreductases 1 and 2, having isoelectric points of 8.45 and 8.6, respectively. A significant amount of zinc was found in the preparation by X-ray fluorescence analysis. The enzyme as it was prepared was colorless, but, after oxidation with p-nitrosophenol followed by gel filtration in the absence of NADH, it showed the absorption spectrum of a flavoprotein. Spectral data indicated the presence of 1 mol of flavin per mol of the enzyme. The molecular turnover number was calculated to be 10,000 nmol p-nitrosophenol reduced to p-aminophenol per min per nmol enzyme at pH 5.8 and 22 degrees C. The activity was inhibited by p-chloromercuribenzoate by 50% at a concentration of 3 x 10(-5) M. Besides the nitrosoreductase activity, the purified preparation showed NAD(P)H-dependent menadione reductase activity. The activities were both strongly inhibited by dicumarol and markedly activated by serum albumin and by Tween 20. These results indicate the probable identity of this enzyme with soluble NAD(P)H dehydrogenase (quinone) [EC 1.6. 99.2].
The Decentralised Coordination of Self-Adaptive Components for Autonomic Distributed Systems

ion Control signal system model Disturbance Inputs Inputs Outputs Services Information Infrastructure Adaptive Architecture Controller Figure 2.9: Hinnelund's model of an autonomic computing system as a control system. autonomic systems as examples of closed-loop control systems (Taylor and Tofts, 2004). Inputs that cannot be controlled directly are called disturbance inputs. Relationships between inputs and outputs can be linear or non-linear, with linear systems being favoured over non-linear systems due to their predictability. State Monitoring A state-space model can be used to describe a control system that has more than one input and/or output. The size of the state-space should be tractable. The monitoring of system states is equivalent in control systems terms to soliciting feedback from system operation in order to guide the adaptive behaviour of the system (Dutton et al., 1997). State information in control systems usually satis es the Markov property (Dutton et al., 1997), as the decision making components generally make decisions without recourse to historical information (Hinnelund, 2004; Dutton et al., 1997). Techniques have been developed, such as estimators and observers (Dutton et al., 1997), to handle situations where measurements of system state cannot be made directly and must be computed from available measurement data. In Hinnelund's model (see gure 2.9) there is no support for an abstract model of system state. He provides a sample autonomic system in (Hinnelund, 2004) that implements a service work ow. In
Interval Estimation For The Scale Parameter Of Burr Type X Distribution Based On Grouped Data

The application of some bootstrap type intervals for the scale parameter of the Burr type X distribution with grouped data is proposed. The general asymptotic confidence interval procedure (Chen & Mi, 2001) is studied. The performance of these intervals is investigated and compared. Some of the bootstrap intervals give better performance for situations of small sample size and heavy censoring.