gebhart/patrepeval huggingface dataset:
Ability of <i>Salmonella</i> spp. to Produce Biofilm Is Dependent on Temperature and Surface Material (2014)

Salmonella, one of the most important pathogens transmitted by food, especially poultry, has the ability to form biofilms on surfaces. Its adhesion can be influenced by different physicochemical properties of these surfaces, while Salmonella uses fimbriae and produces cellulose as the main matrix components of biofilms. Their synthesis is co-regulated by a LuxR-type regulator, the agfD (aggregative fimbriae, curli), and adrA genes, respectively. Thus, this study investigated the production of biofilm by Salmonella spp. isolated from raw poultry (breast fillet), purchased in Botucatu, Sao Paulo, Brazil, on glass, polyvinyl chloride, and stainless steel at different temperatures (16°, 20°, 28°, and 35°C). We analyzed the frequency of the agfD and adrA genes and the rdar morphotype at 28°C and 35°C in isolated strains. We found Salmonella in 112 of 240 poultry samples (46.7%), and 62 strains previously isolated from the same kind of food were included in the study on biofilm development, gene expression, and rdar morphotype. All of them were positive for both genes, and 98.3% were able to produce biofilm in at least one temperature. The rates of rdar morphotype at 28°C and at 35°C were 55.2% (96 strains) and 2.3% (4 strains), respectively. Glass was the best material to avoid biofilm production, while Salmonella grew even at 16°C on stainless steel. These results point out the need for more effective sanitizing processes in the slaughter plants in order to avoid the permanence of these bacteria in food and eventual human foodborne diseases.
Role of the <i>Pseudomonas aeruginosa oxyR-recG</i> Operon in Oxidative Stress Defense and DNA Repair: OxyR-Dependent Regulation of <i>katB-ankB</i> , <i>ahpB</i> , and <i>ahpC-ahpF</i> (2000)

Pseudomonas aeruginosa possesses an extensive armament of genes involved in oxidative stress defense, including katB-ankB, ahpB, and ahpC-ahpF. Transcription of these genes was regulated in response to H(2)O(2), paraquat, or organic peroxides. Expression of katB-lacZ and the observed KatB catalase levels in P. aeruginosa PAO1 were induced up to 250-fold after exposure to oxidative stress-generating compounds. Also, ahpB-lacZ and ahpC-lacZ expression was 90- and 3-fold higher, respectively, upon exposure to paraquat. The dose- and time-response curves revealed that 1 microM paraquat was sufficient for half-maximal activation of each reporter fusion within 5 min of exposure. Expression of these genes was not observed in a DeltaoxyR mutant, indicating that OxyR was essential for this response. The transcriptional start sites of katB-ankB, ahpB, and ahpC-ahpF were mapped, putative OxyR-binding sites were identified upstream of the -35 promoter elements, and direct binding of purified OxyR protein to these target promoters was demonstrated. The oxyR mutant was hypersusceptible to oxidative stress-generating agents, including H(2)O(2) and paraquat, in spite of total KatA catalase activity being comparable to that of the wild type. The oxyR phenotype was fully complemented by a plasmid containing the oxyR gene, while any of the katB, ahpB, or ahpCF genes alone resulted in only marginal complementation. Increased katB-lacZ expression and higher KatB catalase levels were detected in a DeltaahpCF background compared to wild-type bacteria, suggesting a compensatory function for KatB in the absence of AhpCF. In P. aeruginosa, oxyR is located upstream of recG, encoding a putative DNA repair enzyme. oxyR-lacZ and recG-lacZ reporter activities and oxyR-recG mRNA analysis showed that oxyR and recG are organized in an operon and expressed constitutively with regard to oxidative stress from a single promoter upstream of oxyR. Mutants affected in recG but not oxyR were dramatically impaired in DNA damage repair as measured by sensitivity to UV irradiation. In conclusion, we present evidence that the oxyR-recG locus is essential for oxidative stress defense and for DNA repair.
Composite Scaffolds for Bone Tissue Engineering (2006)

Biomaterial and scaffold development underpins the advancement of tissue engineering. Traditional scaffolds based on biodegradable polymers such as poly(lactic acid) and poly(lactic acid-co-glycolic acid) are weak and non-osteoconductive. For bone tissue engineering, polymer-based composite scaffolds containing bioceramics such as hydroxyapatite can be produced and used. The bioceramics can be either incorporated in the scaffolds as a dispersed secondary phase or form a thin coating on the pore surface of polymer scaffolds. This bioceramic phase renders the scaffolds bioactive and also strengthens the scaffolds. There are a number of methods that can be used to produce bioceramic-polymer composite scaffolds. This paper gives an overview of our efforts in developing composite scaffolds for bone tissue engineering.
Silica-based microstructures on nonplanar substrates by femtosecond laser-induced nonlinear lithography (2009)

We developed a technique for the formation of nonplanar surfaces of inorganic optical materials by a combined process of nonlinear lithography and plasma etching. This technique can be used to fabricate structures even on non-flat substrates, which is difficult using current semiconductor technology. Three-dimensional patterns were written directly inside a positive-tone photoresist using femtosecond laser-induced nonlinear optical absorption. The patterns were then transferred to underlying nonplanar substrates by the ion beam etching technique. For the lithographic process, we obtained a minimum feature size of 900 nm, which is below the diffraction limit. We demonstrated the fabrication of silica-based hybrid diffractive-refractive lenses. Fresnel zone plates with smooth surfaces were obtained on convex microlenses. When a 633-nm-wavelength He-Ne laser was coupled normally to the hybrid lens, the primary focal length was measured as 630 μm. This hybridization shifted the focal length by 200 μm, which agreed with the theoretical value. Our process is useful for the precise fabrication of nonplanar structures based on inorganic materials.
Biofilm-Related Infections: Bridging the Gap between Clinical Management and Fundamental Aspects of Recalcitrance toward Antibiotics (2014)

Surface-associated microbial communities, called biofilms, are present in all environments. Although biofilms play an important positive role in a variety of ecosystems, they also have many negative effects, including biofilm-related infections in medical settings. The ability of pathogenic biofilms to survive in the presence of high concentrations of antibiotics is called "recalcitrance" and is a characteristic property of the biofilm lifestyle, leading to treatment failure and infection recurrence. This review presents our current understanding of the molecular mechanisms of biofilm recalcitrance toward antibiotics and describes how recent progress has improved our capacity to design original and efficient strategies to prevent or eradicate biofilm-related infections.
Harmonic compensation in a load emulation system using different control techniques (2012)

In this paper harmonic current control in a power electronic based load emulation system is presented. Purpose of the load emulation system is to carry out full load tests of power electronic systems under realistic conditions, while the energy yield of the device under test is fed back the power grid. Harmonic currents drawn by the device under test from the power grid need to be compensated by the energy feedback converter in order to protect the grid from unduly high harmonic currents. Three different harmonic current controllers have been investigated and compared using experimental results of an 160kVA load emulation system.
Application of a Granular Mineral-Based Hemostatic Agent (QuikClot) to Reduce Blood Loss After Grade V Liver Injury in Swine (2004)

QuikClot provides hemostasis and decreased mortality in this model of severe liver injury. The beneficial aspects of QuikClot treatment must, however, be balanced against the tissue-damaging effects of the exothermic reaction.
The Role of Fullerene-Like Structures in Carbon Black and Their Interaction with Dienic Rubber (2000)

Abstract The identification of fullerene-like sites on carbon black surface and in particular the pentagonal or corannulene-type sites, has permitted us to explain the chemical interaction between filler and polymer (diene rubber) occurring during mixing in terms of free radical and Diels-Alder addition of polymer chains on the fullerene-like sites of carbon black. The free radicals and diene sites are formed on rubber chains during mixing by the mechanochemical degradation, which is caused by shear stresses. We have also noticed the curious analogy between the turbostratic morphology of carbon black particles and the onion-like graphitic particles.
The Magnetoviscoelastic Response of Elastomer Composites Consisting of Ferrous Particles Embedded in a Polymer Matrix (1996)

The mechanical response of elastomer composites to applied magnetic fields is examined. These elastomer composites consist of carbonyl iron particles embedded within a molded elastomer matrix. The composite is subjected to a strong magnetic field during curing, which causes the iron particles to form columnar structures that are parallel to the applied field. This special composite geometry is known to enhance the mechanical response to the application of post-cured magnetic fields. Experimental data is presented that shows that up to a 0.6 MPa change in mechanical shear modulus (which represents 30-40% change in modulus for the materials tested) is possible in response to an applied magnetic field for a composite containing 30% (V/V) iron particles. A simple quasi-static dipole model is presented to examine the magnetoviscoelastic effect of these elastomer composites. The model is semi-empirical in that it may be fit to experimental data over a broad range of applied fields by adjusting a parameter that accounts for unmodeled multipolar magnetic interactions between particles within the composite. Such elastomer composites hold promise in enabling variable stiffness devices and adaptive structures.
Multicast in 3G networks: (2002)

In this article we discuss the use of commonly deployed IP multicast protocols in UMTS networks. We analyze three possible UMTS multicast architectures, all employing standard IP multicast protocols. We study the architectures' ability to handle: group management, data-security, authentication and authorization of multicast source/receivers, multicast session identification, terminal mobility and collection of billing data. For one of the architectures we quantify the performance of the design for two multimedia service examples.
A Guide to Surface Features Related to Underground Coal Mining (2013)

The purpose of this guide is to assist investigators conducting geologic hazard assessments with the understanding, detection, and characterization of surface features related to subsidence from underground coal mining. Subsidence related to underground coal mining can present serious problems to new and/or existing infrastructure, utilities, and facilities. For example, heavy equipment driving over the ground surface during construction processes may punch into voids created by sinkholes or cracks, resulting in injury to persons and property. Abandoned underground mines also may be full of water, and if punctured, can flood nearby areas. Furthermore, the integrity of rigid structures such as buildings, dams and bridges may be compromised if mining subsidence results in differential movement at the ground surface. Subsidence of the ground surface is a phenomenon associated with the removal of material at depth, and may occur coincident with mining, gradually over time, or sometimes suddenly, long after mining operations have ceased (Gray and Bruhn, 1984). The spatial limits of underground coal mines may extend for great distances beyond the surface operations of a mine, in some cases more than 10 miles for an individual mine. When conducting geologic hazard assessments, several remote investigation methods can be used to observe surface features related to underground mining subsidence. LiDAR-derived DEMs are generally the most useful method available for identifying these features because the bare earth surface can be viewed. However, due to limitations in the availability of LiDAR data, other methods often need to be considered when investigating surface features related to underground coal mining subsidence, such as Google Earth and aerial imagery. Mine maps, when available, can be viewed in tandem with these datasets, potentially improving the confidence of any possible mining subsidence-related features observed remotely. However, maps for both active and abandoned mines may be incomplete or unavailable. Therefore, it is important to be able to recognize possible surface features related to underground mining subsidence. This guide provides examples of surface subsidence features related to the two principal underground coal mining methods used in the United States: longwall mining and room and pillar mining. The depth and type of mining, geologic conditions, hydrologic conditions, and time are all factors that may influence the type of features that manifest at the surface. This guide provides investigators a basic understanding about the size, character and conditions of various surface features that occur as a result of underground mining subsidence.
<i>In vitro</i> and <i>In vivo</i> Antitumor Effects of the Dual Insulin-Like Growth Factor-I/Insulin Receptor Inhibitor, BMS-554417 (2006)

The insulin-like growth factor receptor (IGF-IR) and insulin receptor are either overactivated and/or overexpressed in a wide range of tumor types and contribute to tumorigenicity, proliferation, metastasis, and drug resistance. Here, we show that BMS-554417, a novel small molecule developed as an inhibitor of IGF-IR, inhibits IGF-IR and insulin receptor kinase activity and proliferation in vitro, and reduces tumor xenograft size in vivo. In a series of carcinoma cell lines, the IC50 for proliferation ranged from 120 nmol/L (Colo205) to >8.5 micromol/L (OV202). The addition of stimulatory ligands was unnecessary for the antiproliferative effect in MCF-7 and OV202 cells. BMS-554417 treatment inhibited IGF-IR and insulin receptor signaling through extracellular signal-related kinase as well as the phosphoinositide 3-kinase/Akt pathway, as evidenced by decreased Akt phosphorylation at Ser473. At doses that inhibited proliferation, the compound also caused a G0-G1 arrest and prevented nuclear accumulation of cyclin D1 in response to LR3 IGF-I. In Jurkat T-cell leukemia cells, this agent triggered apoptotic cell death via the mitochondrial pathway. BMS-554417 was orally bioavailable and significantly inhibited the growth of IGF1R-Sal tumor xenografts in vivo. BMS-554417 is a member of a novel class of IGF-IR/insulin receptor inhibitors that have potential clinical applications because of their antiproliferative and proapoptotic activity in vitro and in vivo.
Biochemical and genetic properties of site-specific restriction endonucleases in Bacillus globigii (1978)

Bacillus globigii contains two site-specific endonucleases, BPGLI AND BglI. A rapid technique for selection of mutants deficient in each of these enzymes was developed using sensitivity to infection by bacteriophage SP50 as an indication of the levels of enzyme. Mutants defective in BglI, BglII, and both BglI and BglII retained the wild-type modification phenotype. Genetic and biochemical studies have established that these enzymes are involved in restriction in vivo. Simplified purification procedures for BglI and BglII using these mutants are described.
The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on<i>Arabidopsis</i>    (2013)

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies.
Ostwald Ripening of Alkane in Water Emulsions Stabilized by Sodium Dodecyl Benzene Sulfonate (2002)

The Ostwald ripening of alkane in water emulsions stabilized by the anionic surfactant sodium dodecyl benzene sulfonate (SDBS) was investigated. For emulsions prepared under high-shear conditions in a microfluidizer, ripening rates do not depend on the micellar surfactant concentration. The aging process is due to the molecular transport of alkane through the continuous phase, and there is no significant contribution from a transport mechanism by the micelles. When micellar surfactant solutions are added to an already formed emulsion, the Ostwald ripening process is not affected, confirming the fact that the micelles do not contribute to the transport of alkane molecules.
Effect of acarbose on insulin sensitivity in elderly patients with diabetes. (2000)

Acarbose increases insulin sensitivity but not insulin release in elderly patients with diabetes.
[Recent progress in fusion enzyme design and applications]. (2012)

Engineering and redesign of enzymes are important to industrial biocatalysis. Fusion enzyme technology, based on fusion protein design, is frequently used in multifunctional enzyme construction and enzyme proximity control. Here, we reviewed the recent progress in molecular design strategy and application studies of fusion enzymes. The concept and features of fusion enzymes were introduced, followed by a systematical summary of the design strategy of fusion enzymes. In particular, the effects of different linker properties on fusion enzymes and their possible mechanisms were discussed. In addition, recent studies on fusion enzyme applications were also discussed. Finally, based on our own studies on fusion enzymes and the current research progress, the key problems in fusion enzyme technology and perspectives of this field were discussed.
Protein‐induced changes during the maturation process of human dendritic cells: A 2‐D DIGE approach (2008)

Dendritic cells (DCs) are unique antigen presenting cells, which upon maturation change from a specialized antigen-capturing cell towards a professional antigen presenting cells. In this study, a 2-D DIGE analysis of immature and mature DCs was performed, to identify proteins changing in expression upon maturation. The protein expression profile of immature and mature DCs, derived from CD14(+) peripheral blood monocytes was investigated using two pH ranges (pH 4-7 and 6-9) (n = 4). Ninety one differentially expressed spots (p<0.01) were detected, from which we identified 74 spots (81.32%) corresponding to 41 different proteins. The proteins identified play a role in diverse processes, such as antigen processing/presentation, vesicle transport and cytoskeleton remodeling. In addition, a protein interaction network contained 29 (out of 41) proteins, suggesting that, although they functionally originate from distinct classes, these proteins are acting as a protein-interactome. In conclusion, the proteins shown here to be altered in expression upon maturation are in line with the morphological and functional changes observed during the maturation process, providing a better understanding of the processes involved. This will open new avenues for investigating treatment regimens for immune-associated disorders.
TDMA‐SDMA‐based RFID algorithm for fast detection and efficient collision avoidance (2017)

Summary In radio frequency identification, collisions between tags and readers are among key weaknesses to address for reliable operation. To efficiently tackle the above issues and shorter the identification time, different algorithms have been adopted. However, they are still perfectible. For this aim, an efficient fast detection and collision avoidance (FD‐CA) algorithm is proposed to solve tag to tag collision drawbacks. Design and Methods Based on an innovative combination of TDMA and SDMA algorithms, it takes into account spatial distribution of tags to significantly reduce their identification time. Results and Discussion Besides, to further highlight its efficiency, the proposed algorithm was successfully applied to reader‐to‐reader collision with an increasing throughput and a decreasing average waiting time and average rate collision while compared to existing algorithms. Conclusion Finally, the proposed FD‐CA was demonstrated through practical examples, comparison with existing works, and successful FPGA implementation.
Mouse Genetics Suggests Cell-Context Dependency for Myc-Regulated Metabolic Enzymes during Tumorigenesis (2012)

c-Myc (hereafter called Myc) belongs to a family of transcription factors that regulates cell growth, cell proliferation, and differentiation. Myc initiates the transcription of a large cast of genes involved in cell growth by stimulating metabolism and protein synthesis. Some of these, like those involved in glycolysis, may be part of the Warburg effect, which is defined as increased glucose uptake and lactate production in the presence of adequate oxygen supply. In this study, we have taken a mouse-genetics approach to challenge the role of select Myc-regulated metabolic enzymes in tumorigenesis in vivo. By breeding λ-Myc transgenic mice, Apc(Min) mice, and p53 knockout mice with mouse models carrying inactivating alleles of Lactate dehydrogenase A (Ldha), 3-Phosphoglycerate dehydrogenase (Phgdh) and Serine hydroxymethyltransferase 1 (Shmt1), we obtained offspring that were monitored for tumor development. Very surprisingly, we found that these genes are dispensable for tumorigenesis in these genetic settings. However, experiments in fibroblasts and colon carcinoma cells expressing oncogenic Ras show that these cells are sensitive to Ldha knockdown. Our genetic models reveal cell context dependency and a remarkable ability of tumor cells to adapt to alterations in critical metabolic pathways. Thus, to achieve clinical success, it will be of importance to correctly stratify patients and to find synthetic lethal combinations of inhibitors targeting metabolic enzymes.