gebhart/patrepeval huggingface dataset:
Isolation and Chemical Characterization of a Capsular Polysaccharide Antigen Shared by Clinical Isolates of Enterococcus faecalis and Vancomycin-Resistant Enterococcus faecium (1999)

Enterococci are a common cause of serious infections, especially in newborns, severely immunocompromised patients, and patients requiring intensive care. To characterize enterococcal surface antigens that are targets of opsonic antibodies, rabbits were immunized with various gentamicin-killed Enterococcus faecalis strains, and immune sera were tested in an opsonophagocytic assay against a selection of clinical isolates. Serum raised against one strain killed the homologous strain (12030) at a dilution of 1:5,120 and mediated opsonic killing of 33% of all strains tested. In addition, this serum killed two (28%) of seven vancomycin-resistant Enterococcus faecium strains. Adsorption of sera with the homologous strain eliminated killing activity. The adsorbing antigens were resistant to treatment with proteinase K and to boiling for 1 h, but were susceptible to treatment with sodium periodate, indicating that the antigen inducing opsonic activity is a polysaccharide. Antibodies in immune rabbit sera reacted with a capsule-like structure visualized by electron microscopy both on the homologous E. faecalis strain and on a vancomycin-resistant E. faecium strain. The capsular polysaccharides from E. faecalis 12030 and E. faecium 838970 were purified, and chemical and structural analyses indicated they were identical glycerol teichoic acid-like molecules with a carbohydrate backbone structure of 6-alpha-D-glucose-1-2 glycerol-3-PO4 with substitution on carbon 2 of the glucose with an alpha-2-1-D-glucose residue. The purified antigen adsorbed opsonic killing activity from immune rabbit sera and elicited high titers of antibodies (when used to immunize rabbits) that both mediated opsonic killing of bacteria and bound to a capsule-like structure visualized by electron microscopy. These results indicate that approximately one-third of a sample of 15 E. faecalis strains and 7 vancomycin-resistant E. faecium strains possess shared capsular polysaccharides that are targets of opsonophagocytic antibodies and therefore are potential vaccine candidates.
Differential regulation of the anthocyanin profile in purple kiwifruit (Actinidia species) (2018)

Anthocyanins are a group of secondary metabolites that colour fruit and flowers orange, red, purple or blue depending on a number of factors, such as the basic structure, co-pigmentation, metal ion complexation and vacuolar pH. The biosynthesis of anthocyanin is regulated at the transcriptional level by a group of transcription factors, the MYB-bHLH-WD40 (MBW) complex. In this study, the purple colouration in several kiwifruit (<i>Actinidia)</i> species was identified and characterised as red cyanidin-based and blue delphinidin-based anthocyanins. The differential pigmentation in the skin and flesh can be attributed to the differential ratio of cyanidin and delphinidin derivatives accumulated in the total anthocyanin profile. The expression of anthocyanin biosynthetic genes chalcone synthase (<i>CHS</i>), flavonoid 3-O-glucosyltransferase (<i>F3GT</i>), flavonoid 3'-hydroxylase (<i>F3</i>'<i>H</i>) and flavonoid 3'5'-hydroxylase (<i>F3</i>'<i>5</i>'<i>H</i>) is crucial for anthocyanin accumulation. However, the balance of expression of the <i>F3</i>'<i>H</i> and <i>F3</i>'<i>5</i>'<i>H</i> genes appears responsible for the ratio of cyanidin and delphinidin derivatives, while a lack of <i>CHS</i>, <i>F3GT</i> and <i>MYB110</i> expression is responsible for a lack of total anthocyanins. The transcriptional regulation of the <i>F3</i>'<i>H</i> and <i>F3</i>'<i>5</i>'<i>H</i> promoters by the R2R3 MYB transcription factor MYB110 is markedly different in tobacco transient assays. When kiwifruit MYB10 or MYB110 are over-expressed in <i>Actinidia chinensis</i> both cyanidin-based and delphinidin-based anthocyanins are elevated, but <i>F3</i>'<i>H</i> and <i>F3</i>'<i>5</i>'<i>H</i> genes are not strongly correlated with MYB expression. These results suggest that the core kiwifruit anthocyanin pathway genes are dependent on characterised MYB transcription factors, while other regulatory proteins are more directly responsible for the expression of the <i>F3</i>'<i>H</i> and <i>F3</i>'<i>5</i>'<i>H</i> genes.
Supplementary Material from Mesothelin is a malignant factor and therapeutic vaccine target for pancreatic cancer (2023)

Supplementary Material from Mesothelin is a malignant factor and therapeutic vaccine target for pancreatic cancer
Increase in Intraepithelial Lymphocytes as an Early Marker of Rejection in a Fully Allogeneic Rat Small Bowel Transplantation Model (1993)

In a model of fully allogeneic heterotopic rat small bowel transplantation, the changes in intraepithelial lymphocyte (IEL) number and subpopulations were analysed. During early phases of rejection (5th postoperative day) a 4-fold increase in the number of IEL was observed when compared with native small bowel (4.05 vs. 15.84 IEL/100 epithelial cells). When cyclosporine was given, counts were still as high as 11.4 and 12.58 on the 5th and 10th postoperative days, respectively. The percentage of CD8+ IEL, constituting a major population (84%) in the untreated small bowel, was significantly decreased (46.4%) during early phases of rejection. At that time, the majority of intraepithelial mononuclear cells were both CD8- and CD4-. In cyclosporine-treated animals, this was not observed until the 10th postoperative day. Some 23% of IEL in untreated animals expressed MHC class I antigens of the host; 17.2% (5th postoperative day) and 19.8% (10th postoperative day) did so in the cyclosporine-treated animals. Transmission electron microscopy revealed lymphocytes that bore cytoplasmic buds and pseudopods protruding between the enterocytes. There was no morphological difference between the IEL of rejected allografts and native small bowel. Due to the unspecific histologic changes associated with rejection, interpretation of histopathologic findings in mucosa biopsies of the allograft can be rather troublesome. An increase in the number of IEL is therefore a welcome additional marker of rejection.
Long-Term Preservation of Cones and Improvement in Visual Function Following Gene Therapy in a Mouse Model of Leber Congenital Amaurosis Caused by Guanylate Cyclase-1 Deficiency (2011)

Leber congenital amaurosis (LCA) is a severe retinal dystrophy manifesting from early infancy as poor vision or blindness. Loss-of-function mutations in GUCY2D cause LCA1 and are one of the most common causes of LCA, accounting for 20% of all cases. Human GUCY2D and mouse Gucy2e genes encode guanylate cyclase-1 (GC1), which is responsible for restoring the dark state in photoreceptors after light exposure. The Gucy2e(-/-) mouse shows partially diminished rod function, but an absence of cone function before degeneration. Although the cones appear morphologically normal, they exhibit mislocalization of proteins involved in phototransduction. In this study we tested the efficacy of an rAAV2/8 vector containing the human rhodopsin kinase promoter and the human GUCY2D gene. Following subretinal delivery of the vector in Gucy2e(-/-) mice, GC1 protein was detected in the rod and cone outer segments, and in transduced areas of retina cone transducin was appropriately localized to cone outer segments. Moreover, we observed a dose-dependent restoration of rod and cone function and an improvement in visual behavior of the treated mice. Most importantly, cone preservation was observed in transduced areas up to 6 months post injection. To date, this is the most effective rescue of the Gucy2e(-/-) mouse model of LCA and we propose that a vector, similar to the one used in this study, could be suitable for use in a clinical trial of gene therapy for LCA1.
Sustainable Ethanol Production From Sugarcane Molasses by Saccharomyces cerevisiae Immobilized on Chitosan-Coated Manganese Ferrite (2021)

The interaction between nanostructures and yeast cells, as well as the description of the effect of nanoparticles in ethanol production are open questions in the development of this nanobiotechnological process. The objective of the present study was to evaluate the ethanol production by Saccharomyces cerevisiae in the free and immobilized state on chitosan-coated manganese ferrite, using cane molasses as a carbon source. To obtain the chitosan-coated manganese ferrite, the one-step coprecipitation method was used. The nanoparticles were characterized by X-ray diffraction obtaining the typical diffraction pattern. The crystal size was calculated by the Scherrer equation as 15.2 nm. The kinetics of sugar consumption and ethanol production were evaluated by HPLC. With the immobilized system, it was possible to obtain an ethanol concentration of 56.15 g/L, as well as the total sugar consumption at 24 h of fermentation. Productivity and yield in this case were 2.3 ± 0.2 g/(L * h) and 0.28 ± 0.03, respectively. However, at the same time in the fermentation with free yeast, 39.1 g/L were obtained. The total consumption of fermentable sugar was observed only after 42 h, reaching an ethanol titer of 50.7 ± 3.1, productivity and yield of 1.4 ± 0.3 g/(L * h) and 0.25 ± 0.4, respectively. Therefore, a reduction in fermentation time, higher ethanol titer and productivity were demonstrated in the presence of nanoparticles. The application of manganese ferrite nanoparticles shows a beneficial effect on ethanol production. Research focused on the task of defining the mechanism of their action and evaluation of the reuse of biomass immobilized on manganese ferrite in the ethanol production process should be carried out in the future.
(2+1)-dimensional stable spatial Raman solitons (2004)

We analyze the formation, propagation, and interaction of stable two-frequency $(2+1)$-dimensional solitons, formed in a Raman media driven near maximum molecular coherence. The propagating light is trapped in the two transverse dimensions.
Adapting publish/subscribe middleware to achieve Gnutella-like functionality (2001)

Gnutella represents a new wave of peer-to-peer applications providing distributed discovery and coordinated sharing of resources across the Internet. Gnutella is distinguished by its support for anonymity and by its decentralized architecture. The current Gnutella architecture and protocol have numerous flaws with respect to efficiency, anonymity, and vulnerability to malicious actions. An alternative design is described providing Gnutella-like functionality but removing or mitigating many of Gnutella's flaws. This design, referred to as Query/Advertise (Q/A) is based upon a scalable Publish/Subscribe middleware system called Siena. A prototype implementation of Q/A is described. The relative benefits of this approach are discussed, and a number of open research problems are identified with respect to Q/A systems.
Phased arrays-part II: implementations, applications, and future trends (2002)

In part I of this paper, we presented the basic architectures and theory for passive and active phased arrays. Here, we review array implementation, state-of-the-art applications, and identify future trends in phased-array technology.
Interarrival time distribution for a non-Markovian arrival process (2008)

We consider a probabilistic model for workload input into a telecommunication system. It captures the dynamics of packet generation in data traffic as well as accounting for long-range dependence and self-similarity exhibited by real traces. The workload has stationary increments as observed in high-speed data networks for certain periods. Such periods with peak demand can be studied with this model for further queuing performance analysis. The workload is found by aggregating the number of packets, or their sizes, generated by the arriving sessions. The arrival time, the duration and the packet generation process of a session are all governed by a Poisson random measure. The model has been recently used in a G/M/1 queuing system with priority where the interarrival time distribution has been approximated. We show that it is a good approximation due to good match of the computed performance measures with the simulation results.
Mechanistic studies on DNA damage by minor groove binding copper-phenanthroline conjugates (2005)

Copper-phenanthroline complexes oxidatively damage and cleave nucleic acids. Copper bis-phenanthroline and copper complexes of mono- and bis-phenanthroline conjugates are used as research tools for studying nucleic acid structure and binding interactions. The mechanism of DNA oxidation and cleavage by these complexes was examined using two copper-phenanthroline conjugates of the sequence-specific binding molecule, distamycin. The complexes contained either one or two phenanthroline units that were bonded to the DNA-binding domain through a linker via the 3-position of the copper ligand. A duplex containing independently generated 2-deoxyribonolactone facilitated kinetic analysis of DNA cleavage. Oxidation rate constants were highly dependent upon the ligand environment but rate constants describing elimination of the alkali-labile 2-deoxyribonolactone intermediate were not. Rate constants describing DNA cleavage induced by each molecule were 11-54 times larger than the respective oxidation rate constants. The experiments indicate that DNA cleavage resulting from beta-elimination of 2-deoxyribonolactone by copper-phenanthroline complexes is a general mechanism utilized by this family of molecules. In addition, the experiments confirm that DNA damage mediated by mono- and bis-phenanthroline copper complexes proceeds through distinct species, albeit with similar outcomes.
Viscoelastic behavior in toluene at high pressure (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTViscoelastic behavior in toluene at high pressureRobert G. Rein, Cedomir M. Sliepcevich, and Stanley E. BabbCite this: J. Chem. Eng. Data 1968, 13, 4, 511–514Publication Date (Print):October 1, 1968Publication History Published online1 May 2002Published inissue 1 October 1968https://pubs.acs.org/doi/10.1021/je60039a015https://doi.org/10.1021/je60039a015research-articleACS PublicationsRequest reuse permissionsArticle Views41Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Sensor models and localization algorithms for sensor networks based on received signal strength (2012)

Received signal strength (RSS) can be used in sensor networks as a ranging measurement for positioning and localization applications. This contribution studies the realistic situation where neither the emitted power nor the power law decay exponent be assumed to be known. The application in mind is a rapidly deployed network consisting of a number of sensor nodes with low-bandwidth communication, each node measuring RSS of signals traveled through air (microphones) and ground (geophones). The first contribution concerns validation of a model in logarithmic scale, that is, linear in the unknown nuisance parameters (emitted power and power loss constant). The parameter variation is studied over time and space. The second contribution is a localization algorithm based on this model, where the separable least squares principle is applied to the non-linear least squares (NLS) cost function, after which a cost function of only the unknown position is obtained. Results from field trials are presented to illustrate the method, together with fundamental performance bounds. The ambition is to pave the way for sensor configuration design and more thorough performance evaluations as well as filtering and target tracking aspects.
Invasion of weedy rice in rice fields in Thailand: problems and management (2004)

This article 'Invasion of weedy rice in rice fields in Thailand: problems and management' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.
Preparation of Titanium Oxide Pillars on Glass Substrates and Ultrathin Titanium Oxide Layer using PMMA/PS Blend Films (2008)

In this paper, a simple and inexpensive method of preparing nanosized titanium oxide (TiO2) pillars on glass substrates and ultrathin TiO2 layers is presented, utilizing a blend of commercially available polystyrene (PS) and poly(methyl methacrylate) (PMMA). The surface morphology of PS/PMMA blend films is investigated in terms of the processing parameters including solution concentration, blending ratio, and spin-coating speed. For the first time, a phase inversion was revealed for the PS/PMMA blend films spun coated on conducting substrates (ITO and TiO2), with increasing solution concentration. Atomic force microscopy studies show that PMMA forms vertical cylindrical structures in the matrix of PS on glass substrates and on ultrathin TiO2 layers deposited on indium tin oxide (ITO) substrates. After the PMMA phase is etched away by ultraviolet irradiation and acetic acid, TiO2 pillar structures are successfully created on both types of substrates by infiltration of the sol−gel mixture into the nanosized PS templates followed by calcination at an elevated temperature. The size and shape of the TiO2 pillars were found to be affected by the thickness and phase separation of the initial PS/PMMA films, which depend on the solution concentration and blending ratio of the two polymeric components.
Diversity, dynamics and activity of mesophilic Archaea in stratified feshwater lakes. Implications in biogeochemical cycles (2010)

Aquesta tesi doctoral va estudiar la diversitat (riquesa i abundancia), la distribucio i la dinamica de les comunitats planctoniques d'Archaea presents a diferents llacs estratificats temperats d'aigua dolca per aportar evidencies sobre la seva distribucio i la seva possible activitat en aquests ecosistemes en relacio als cicles biogeoquimics presents en els mateixos. Es varen estudiar dos estanyols d'origen carstic (l'Estanyol del Vilar durant cinc anys consecutius (2001-2005) i l'Estanyol de Can Coromina) i un llac d'origen volcanic (Llac Kivu) analitzant, per una banda, la seva comunitat planctonica d'Archaea mitjancant una aproximacio molecular i, per una altra, la seva possible activitat en aquests ambients (p.e., la nitrificacio i la fixacio de carboni). Per contextualitzar els resultats, es va realitzar un analisi in silico dels patrons de distribucio global dels Archaea mesofils mitjancant un analisi a nivell de llinatge combinant sequencies del gen 16S rRNA amb diferents eines estadistiques i d'ecologia general.
QuLa: Service Selection and Forwarding Table Population in Service-Centric Networking Using Real-Life Topologies (2016)

The amount of services located in the network has drastically increased over the last decade which is why more and more datacenters are located at the network edge, closer to the users. In the current Internet it is up to the client to select a destination using a resolution service (Domain Name System, Content Delivery Networks). In the last few years, research on Information-Centric Networking (ICN) suggests to put this selection responsibility at the network components, routers find the closest copy of a content object using the content name as input. We extend the principle of ICN to services, service routers forward requests to service instances located in datacenters spread across the network edge. To solve this problem, we first present a service selection algorithm based on both server and network metrics. Next, we describe a method to reduce the state required in service routers while minimizing the performance loss caused by this data reduction. Simulation results based on real-life networks show that we are able to find a near-optimal load distribution with only minimal state required in the service routers.
Integrating the porcine physical and linkage map using cosmid‐derived markers (1994)

An essential part in the development of informative linkage maps is to include genetic markers that have been anchored by physical mapping. Here a set of 18 porcine cosmid-derived genetic markers are reported that have been mapped by linkage analysis, and that also have been physically localized by fluorescence in situ hybridization (FISH). Three different strategies were used to establish polymorphic markers from the cosmid clones. Firstly, dinucleotide microsatellite loci were derived by sequencing cosmid subclones containing (CA)n repeats. Secondly, variable SINE 3' poly(A) tracts (SINEVA) were identified by direct SINE-PCR amplification of cosmid clones. Thirdly, the cosmids were used in Southern blot hybridization to detect restriction fragment length polymorphisms (RFLPs). Compared with the most recent consensus compilation of the porcine gene map, the present assignment of markers to chromosomes 2p, 3, 4, 10, 12q, and 16 represents the first loci mapped to these chromosomes, for which linkage as well as in situ data are now available.
Nonlinear games: examples and counterexamples (2002)

Popular nonlinear control methodologies are compared using benchmark examples generated with a "converse Hamilton-Jacobi-Bellman" method (CoHJB). Starting with the cost and optimal value function V, CoHJB solves HJB PDEs "backwards" algebraically to produce nonlinear dynamics and optimal controllers and disturbances. Although useless for design, it is great for generating benchmark examples. It is easy to use, computationally tractable, and can generate essentially all possible nonlinear optimal control problems. The optimal control and disturbance are then known and can be used to study actual design methods, which must start with the cost and dynamics without knowledge of V. This paper gives a brief introduction to the CoHJB method and some of the ground rules for comparing various methods. Some very simple examples are given to illustrate the main ideas. Both Jacobian linearization and feedback linearization combined with linear optimal control are used as "strawmen" design methods.
Teach–Discover–Treat (TDT): Collaborative computational drug discovery for neglected diseases (2012)

Teach-Discover-Treat (TDT) is an initiative to promote the development and sharing of computational tools solicited through a competition with the aim to impact education and collaborative drug discovery for neglected diseases. Collaboration, multidisciplinary integration, and innovation are essential for successful drug discovery. This requires a workforce that is trained in state-of-the-art workflows and equipped with the ability to collaborate on platforms that are accessible and free. The TDT competition solicits high quality computational workflows for neglected disease targets, using freely available, open access tools.