Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characterization of Streptococcus pneumoniae Type 4, 6B, 8, and 18C Capsular Polysaccharide Gene Clusters

ABSTRACT Capsular polysaccharide (CPS) is a major virulence factor inStreptococcus pneumoniae. CPS gene clusters of S. pneumoniae types 4, 6B, 8, and 18C were sequenced and compared with those of CPS types 1, 2, 14, 19F, 19A, 23F, and 33F. All have the same four genes at the 5′ end, encoding proteins thought to be involved in regulation and export. Sequences of these genes can be divided into two classes, and evidence of recombination between them was observed. Next is the gene encoding the transferase for the first step in the synthesis of CPS. The predicted amino acid sequences of these first sugar transferases have multiple transmembrane segments, a feature lacking in other transferases. Sugar pathway genes are located at the 3′ end of the gene cluster. Comparison of the four dTDP-l-rhamnose pathway genes (rml genes) of CPS types 1, 2, 6B, 18C, 19F, 19A, and 23F shows that they have the same gene order and are highly conserved. There is a gradient in the nature of the variation of rml genes, the average pairwise difference for those close to the central region being higher than that for those close to the end of the gene cluster and, again, recombination sites can be observed in these genes. This is similar to the situation we observed for rml genes of O-antigen gene clusters of Salmonella enterica. Our data indicate that the conserved first four genes at the 5′ ends and the relatively conservedrml genes at the 3′ ends of the CPS gene clusters were sites for recombination events involved in forming new forms of CPS. We have also identified wzx and wzy genes for all sequenced CPS gene clusters by use of motifs.
Ascending and descending stairs for a biped robot

This paper synthesizes an efficient walking pattern for a practical biped robot when ascending and descending stairs. The main features of the biped robot include variable length legs and a translatable balance weight in the body. The biped robot's walk is a mixture of both statically stable and dynamically stable modes and relies on some degrees of static stability provided by large feet and by carefully controlling the center of gravity's position. The paper describes the design and experiment of a 7-DOF practical biped which is capable of ascending and descending stairs, and the synthesis of an efficient walking gait for ascending and descending stairs. Our biped robot is one of the few biped walking machines capable of ascending and descending stairs.
Non-traditional Functions of Ubiquitin and Ubiquitin-binding Proteins*

Until recently, proteasome-mediated proteolysis dominated discussion about the function of ubiquitin, a highly conserved 76-amino acid polypeptide. However, a spate of new discoveries has opened up research into the functions of ubiquitin in regulating proteins by proteasome-independent processes. These investigations have led to a deeper understanding of the different types of ubiquitin modifications and of proteins that bind to monoubiquitin and polyubiquitin chains. In this review we discuss proteasome-independent functions of ubiquitin with emphasis on how monoubiquitin and ubiquitin-binding proteins signal changes in protein location, activity, and interactions with binding partners.
Defining the Wildland-Urban Interface

from the ability to locate and compare the WUI in different states and regions. To support this aspect of WUI management and strategic planning, we created a map of the WUI across the lower 48 states (Radeloff et al. 2005b). Unlike a community-level WUI map that can be enriched by using detailed local data, this “big picture” national map required nationally consistent data and a single standardized WUI definition. Here, we sought to understand how the national WUI map is influenced by the WUI definition used, the relative effect of each part of the definition, and the overall usefulness of the map in identifying homes likely to be affected by wildfire. We used geographic information system (GIS) analysis to address
Bark Characterisation of the Brazilian Hardwood Goupia glabra in Terms of Its Valorisation

The bark of Goupia glabra trees grown in a native forest area in the Amazon region of Brazil was anatomically and chemically characterised for potential use as a chemical source for bio-refineries. The bark is silvery-grey to reddish-grey, with a scaly rhytidome composed of 2 to 3 periderms with a small phellem content. The phloem has abundant sieve tube members and a conspicuous presence of sclerified nodules of fiber-sclereids or sclereids; no fibers were observed. The bark had the following average composition (dry mass): 5.2% ash, 24.6% total extractives, 1.1% suberin, and 43.8% total lignin. The polysaccharide composition showed a high ratio of xylan hemicelluloses to cellulose. The ethanol-water bark extract showed high antioxidant capacity. The chemical characterisation of different granulometric fractions showed that extractives were present preferentially in the finest fractions, particularly with enrichment in ethanol solution.
Microtubule-disrupting drugs blocked delivery of endocytosed transferrin to the cytocenter, but did not affect return of transferrin to plasma membrane.

The fluorescence of FL cells after endocytosis of rhodamine-labeled transferrin initially appeared as a dispersed punctate pattern over the whole cell and then accumulated in the cytocenter on further incubation. In nocodazole-treated cells, the punctate fluorescence appeared along the cell edges, and stayed there on further incubation but did not accumulate in the cytocenter. The localization of transferrin was examined at the electron microscopic level with horseradish peroxidase (HRP)-labeled transferrin. Nocodazole did not affect endosome formation but affected the distribution of the endosomes. Several types of endosomes (tubular, small spherical, and microvesicular endosomes) were observed in nocodazole-treated cells, as in control cells. The endosomes were in the Golgi area of the cytocenter and also in peripheral cytoplasm in control cells. In contrast, the endosomes were only in the periplasm, along the cell edges, in nocodazole-treated cells. The uptake and release of HRP-transferrin and the release of ferric ion into the cytoplasm in nocodazole-treated cells followed in the same time-course as those in control cells. The release of transferrin was the exponential with a half-time of 12 min. The activation energy of a rate-limiting step in the recycling was 5.5 kcal.mol-1 at around 37 degrees C and increased to 29 kcal.mol-1 below 25 degrees C. These results indicated that microtubule-dependent endosome transport was faster than the overall recycling process and was independent of the return event of transferrin to the plasma membrane.
A formal framework for the specification, analysis and generation of standardized hypermedia documents

Proposes a formal framework for the specification, analysis and generation of standardized hypermedia documents. This framework is based on the hierarchical time stream Petri net (HTSPN) model adapted to the specification of temporal and logical constraints in distributed hypermedia systems. The interpreted HTSPN model presented in the paper allows the accurate and unambiguous specification of hypermedia documents. Moreover, it permits powerful analysis techniques to be applied for insuring the quality of hypermedia documents. It is important for a HTSPN specification to be stored, exchanged and presented within open hypermedia systems. Therefore, a procedure for translating interpreted HTSPN specification into an MHEG (Multimedia and Hypermedia Experts Group) representation is also proposed.
A 1 V BiCMOS rail-to-rail amplifier with n-channel depletion-mode input-stage

This amplifier is fabricated on a SMARTMOS/sup TM/ flow with depletion-mode nMOS, vertical p-n-p, and high-frequency n-p-n transistors. Most techniques for achieving rail-to-rail input stage performance concentrate on the use of complementary bipolar or enhancement MOSFET devices to allow the amplifier common-mode range to include both supply rails. These techniques require a minimum supply voltage of 1.8 V for bipolar and 3 V for CMOS to allow a transition from sensing common mode voltages at ground when the p-n-p or pMOS pair is active, to sensing common-mode voltages at the positive supply when the n-p-n or nMOS pair is active. This amplifier uses a single pair of depletion-mode nMOS devices to allow low-voltage, rail-to-rail operation.
Hinge‐helix formation and DNA bending in various lac repressor–operator complexes

The hinge‐region of the lac repressor plays an important role in the models for induction and DNA looping in the lac operon. When lac repressor is bound to a tight‐binding symmetric operator, this region forms an α‐helix that induces bending of the operator. The presence of the hinge‐helices is questioned by previous data that suggest that the repressor does not bend the wild‐type operator. We show that in the wild‐type complex the hinge‐helices are formed and the DNA is bent, similar to the symmetric complex. Furthermore, our data show differences in the binding of the DNA binding domains to the half‐sites of the wild‐type operator and reveal the role of the central base‐pair of the wild‐type operator in the repressor–operator interaction. The differences in binding to the operator half‐sites are incorporated into a model that explains the relative affinities of the repressor for various lac operator sequences that contain left and right half‐sites with different spacer lengths.
Affective Aspects of Perceived Loss of Control and Potential Implications for Brain-Computer Interfaces

Most brain-computer interfaces (BCIs) focus on detecting single aspects of user states (e.g., motor imagery) in the electroencephalogram (EEG) in order to use these aspects as control input for external systems. This communication can be effective, but unaccounted mental processes can interfere with signals used for classification and thereby introduce changes in the signal properties which could potentially impede BCI classification performance. To improve BCI performance, we propose deploying an approach that potentially allows to describe different mental states that could influence BCI performance. To test this approach, we analyzed neural signatures of potential affective states in data collected in a paradigm where the complex user state of perceived loss of control (LOC) was induced. In this article, source localization methods were used to identify brain dynamics with source located outside but affecting the signal of interest originating from the primary motor areas, pointing to interfering processes in the brain during natural human-machine interaction. In particular, we found affective correlates which were related to perceived LOC. We conclude that additional context information about the ongoing user state might help to improve the applicability of BCIs to real-world scenarios.
PARALLEL PROCESSING OF LARGE DATA SETS IN PARTICLE PHYSICS

The analysis of the LHC data aims to minimize the vast amounts of data and the number of observables used. After slimming and skimming the data, the remaining terabytes of ROOT files hold a selection of the events and a flat structure for the variables needed that can be more easily inspected and traversed in the final stages of the analysis. PROOF has an efficient mechanism to distribute the analysis load by taking advantage of all the cores in modern CPUs through PROOF-Lite, PROOF Cluster or PROOF on Demand tools. In this paper we compared performance of different methods of file access (NFS, XROOTD, RFIO). The tests were done on Bucharest ATLAS Analysis Facility.
Theoretical Characterization and System Impact of the Hinge Model of PMD

Modeling of the polarization-mode dispersion (PMD) temporal changes in long fiber routes represents a critical aspect of system outage characterization. In this paper, an analysis of the PMD temporal statistics in links obeying the recently proposed hinge model is presented. The analytical expression of the differential group delay probability density function is derived and used to show that the outage probability is channel specific in a wavelength-division-multiplexed system. The existence of outage-free channels, which represents one of the most important implications of the hinge model, is demonstrated and quantified. The frequency dependence of the temporal statistics is also characterized, and an expression for PMD-induced pulse broadening is derived
Divalent Cations in Native and Reaggregated Mycoplasma Membranes

The Mg2+ content of membranes of several Mycoplasma and Acholeplasma species varied between 0.88 and 1.98 μg of Mg2+ per mg of protein, depending on the species and on growth conditions. Ca2+ could be detected only when it was added to the growth medium. The Mg2+ content of isolated A. laidlawii membranes could be increased almost threefold by dialysis against 20 mm Mg2+, whereas aggregated A. laidlawii membranes contained about six to eight times more Mg2+ per mg of protein than the native membranes. This was taken to indicate that the molecular organization of the lipid and protein in the reaggregated membranes differs from that of the native membranes. Between 60 and 83% of the Mg2+ in native and reaggregated A. laidlawii membranes was associated with the lipid fraction extracted with chloroform-methanol. The removal of over 80% of membrane protein by Pronase digestion did not release any significant amount of Mg2+. Hence, most of the divalent cation appears to be bound to membrane lipids, most probably to phospholipids. Ethylenediaminetetraacetic acid released the bulk of Mg2+ bound to the native and reaggregated A. laidlawii membranes, except for about 0.5 μg of Mg2+ per mg of protein which was too tightly bound. Hence, a small but fairly constant amount of Mg2+ is unavailable for chelation.
A Study and Implementation of a Movie Recommendation System in a Cloud-based Environment

The availability of huge amounts of data in recent years have led users to being faced with an overload of choices. The outcome is a growth on the importance of recommendation systems due to their ability to solve this choice overload problem, by providing users with the most relevant products from many possible choices. For producing recommendations, things like a user’s psychological profile, their browsing history and movie ratings from other users can be considered. To determine how strongly two user’s behavior are related to each other, a Pearson correlation coefficient value is often calculated. In this paper, we study the recommendation system on a proposed cloud based environment to produce a list of recommended movies based on a user’s profile information. Based on the Software-as-aService (SaaS) model implemented, we discuss the concepts such as collaborative filtering and content-based filtering. Given a MovieLens data-set, our results indicate that the proposed approach can provide a high performance in terms of precision, and generate more reliable and personalized movie recommendations, when given a greater number of movies rated by a user. An evaluation was done under minimal known data, which commonly leads to the cold-start problem. KEywoRdS Collaborative Filtering, Content Filtering, Pearson Correlation Formula, Recommendation Systems
Prevalence of Gastrointestinal Bacterial Pathogens in a Population of Zoo Animals

Faecal prevalence of gastrointestinal bacterial pathogens, including Campylobacter, Escherichia coli O157:H7, Salmonella, Shigella, Yersinia, as well as Arcobacter, were examined in 317 faecal specimens from 44 animal species in Belfast Zoological Gardens, during July–September 2006. Thermophilic campylobacters including Campylobacter jejuni, Campylobacter coli and Campylobacter lari, were the most frequently isolated pathogens, where members of this genus were isolated from 11 animal species (11 of 44; 25%). Yersinia spp. were isolated from seven animal species (seven of 44; 15.9%) and included, Yersinia enterocolitica (five of seven isolates; 71.4%) and one isolate each of Yersinia frederiksenii and Yersinia kristensenii. Only one isolate of Salmonella was obtained throughout the entire study, which was an isolate of Salmonella dublin (O 1,9,12: H g, p), originating from tiger faeces after enrichment. None of the animal species found in public contact areas of the zoo were positive for any gastrointestinal bacterial pathogens. Also, water from the lake in the centre of the grounds, was examined for the same bacterial pathogens and was found to contain C. jejuni. This study is the first report on the isolation of a number of important bacterial pathogens from a variety of novel host species, C. jejuni from the red kangaroo (Macropus rufus), C. lari from a maned wolf (Chrysocyon brachyurus), Y. kristensenii from a vicugna (Vicugna vicugna) and Y. enterocolitica from a maned wolf and red panda (Ailurus fulgens). In conclusion, this study demonstrated that the faeces of animals in public contact areas of the zoo were not positive for the bacterial gastrointestinal pathogens examined. This is reassuring for the public health of visitors, particularly children, who enjoy this educational and recreational resource.
Structure and Kinetics of Monofunctional Proline Dehydrogenase from Thermus thermophilus*

Proline dehydrogenase (PRODH) and Δ1-pyrroline-5-carboxylate dehydrogenase (P5CDH) catalyze the two-step oxidation of proline to glutamate. They are distinct monofunctional enzymes in all eukaryotes and some bacteria but are fused into bifunctional enzymes known as proline utilization A (PutA) in other bacteria. Here we report the first structure and biochemical data for a monofunctional PRODH. The 2.0-Å resolution structure of Thermus thermophilus PRODH reveals a distorted (βα)8 barrel catalytic core domain and a hydrophobic α-helical domain located above the carboxyl-terminal ends of the strands of the barrel. Although the catalytic core is similar to that of the PutA PRODH domain, the FAD conformation of T. thermophilus PRODH is remarkably different and likely reflects unique requirements for membrane association and communication with P5CDH. Also, the FAD of T. thermophilus PRODH is highly solvent-exposed compared with PutA due to a 4-Å shift of helix 8. Structure-based sequence analysis of the PutA/PRODH family led us to identify nine conserved motifs involved in cofactor and substrate recognition. Biochemical studies show that the midpoint potential of the FAD is -75 mV and the kinetic parameters for proline are Km = 27 mm and kcat = 13 s-1. 3,4-Dehydro-l-proline was found to be an efficient substrate, and l-tetrahydro-2-furoic acid is a competitive inhibitor (KI = 1.0 mm). Finally, we demonstrate that T. thermophilus PRODH reacts with O2 producing superoxide. This is significant because superoxide production underlies the role of human PRODH in p53-mediated apoptosis, implying commonalities between eukaryotic and bacterial monofunctional PRODHs.
Fluorescence of dental hard tissue and restorative materials

emitted in the range of visible light. In UV light a natural tooth emits a weak whitish-blue fluorescence. This should be taken into account when selecting restoratives. If restorative materials do not offer this property of fluorescence, they will look dark in UV light, and the restored tooth (Figure 1) will stand out against the other teeth in the mouth (Figure 2). The fluorescence spectrum of a composite may be violet or blue-green in colour. In addition, the fluorescence intensity of the restorative materials may differ from that of the dental hard tissue (Figures 3 and 4). To ensure a high-quality aesthetic result, the selected restorative should therefore have fluorescence properties resembling those of a natural tooth.
Building Sentiment Lexicon for Social Media Analysis using Morphological Sentence Pattern Model

YouTube is dramatically increasing by various industries for a marketing purpose. Sentiment analysis is aimed to analyze the textual data. It can be used to observe and summarize information from the social media data. However, building lexicon without human-coding efforts is one of challenge for a lexicon based sentiment analysis. In this study, we proposed an approach for building sentimental lexicon using the morphological sentence pattern model for analyzing social media data.
Hybridizable discontinuous Galerkin method for curved domains

In this work we present a technique to numerically solve partial differential equations (PDE’s) defined in general domains Ω. It basically consists in approximating the domain Ω by polyhedral subdomains Dh and suitably defining extensions of the solution from Dh to Ω. More precisely, we solve the PDE in Dh by using a numerical method for polyhedral domains. In order to do that, the boundary condition is transferred from Γ := ∂Ω to Γh, the boundary of Dh, by integrating the gradient of the scalar variable along a path. That is why, in principle, any numerical method that provides an accurate approximation of the gradient can be used. In this work we consider a hybridizable discontinuous Galerkin (HDG) method. This technique has two main advantages over other methods in the literature. First of all, it only requires the distance between Γ and Γh to be of the order of the meshsize. This allows us to easily mesh the computational domain. Moreover, high degree polynomial approximations can be used and still obtain optimal orders of convergence even though Γh is “far” from Γ. We numerically explore this approach by considering three types of steady-state equations. As starting point, we deal with Dirichlet boundary problems for second order elliptic equations. For this problem we fully explain how to properly transfer the boundary condition and how to define the paths, as well. We then apply this technique to exterior diffusion problems. Herein, the HDG method is used for solving the so-called interior problem on a bounded region whereas a boundary element method (BEM) is used for solving the problem exterior to that region. Both methods are coupled at the smooth interface that divides the two regions. Finally, we consider convectiondiffusion problems where we explore how the magnitude of the convective field affects the performance of our method.