gebhart/patrepeval huggingface dataset:
Vaccination with Plasmid DNA Encoding TSA/LmSTI1 Leishmanial Fusion Proteins Confers Protection against<i>Leishmania major</i>Infection in Susceptible BALB/c Mice (2002)

We have recently shown that a cocktail containing two leishmanial recombinant antigens (LmSTI1 and TSA) and interleukin-12 (IL-12) as an adjuvant induces solid protection in both a murine and a nonhuman primate model of cutaneous leishmaniasis. However, because IL-12 is difficult to prepare, is expensive, and does not have the stability required for a vaccine product, we have investigated the possibility of using DNA as an alternative means of inducing protective immunity. Here, we present evidence that the antigens TSA and LmSTI1 delivered in a plasmid DNA format either as single genes or in a tandem digene construct induce equally solid protection against Leishmania major infection in susceptible BALB/c mice. Immunization of mice with either TSA DNA or LmSTI1 DNA induced specific CD4(+)-T-cell responses of the Th1 phenotype without a requirement for specific adjuvant. CD8 responses, as measured by cytotoxic-T-lymphocyte activity, were generated after immunization with TSA DNA but not LmSTI1 DNA. Interestingly, vaccination of mice with TSA DNA consistently induced protection to a much greater extent than LmSTI1 DNA, thus supporting the notion that CD8 responses might be an important accessory arm of the immune response for acquired resistance against leishmaniasis. Moreover, the protection induced by DNA immunization was specific for infection with Leishmania, i.e., the immunization had no effect on the course of infection of the mice challenged with an unrelated intracellular pathogen such as Mycobacterium tuberculosis. Conversely, immunization of BALB/c mice with a plasmid DNA that is protective against challenge with M. tuberculosis had no effect on the course of infection of these mice with L. major. Together, these results indicate that the protection observed with the leishmanial DNA is mediated by acquired specific immune response rather than by the activation of nonspecific innate immune mechanisms. In addition, a plasmid DNA containing a fusion construct of the two genes was also tested. Similarly to the plasmids encoding individual proteins, the fusion construct induced both specific immune responses to the individual antigens and protection against challenge with L. major. These results confirm previous observations about the possibility of DNA immunization against leishmaniasis and lend support to the idea of using a single polygenic plasmid DNA construct to achieve polyspecific immune responses to several distinct parasite antigens.
Study of bioheat transfer phase change during cryosurgery for an irregular tumor tissue using EFGM (2017)

Cryosurgery has been consistently used as an effective treatment to eradicate irregular tumor tissues. During this process, many difficulties occur such as intense cooling may also damage the neighboring normal tissues due to the release of large amount of cold from the cooling probe. In order to protect the normal tissues in the vicinity of target tumor tissues, coolant was released in a regulated manner accompanied with the nanoparticle to regulate the size and orientation of ice balls formed together with improved probe capacity. The phase change occurs in the target tumor tissues during cryosurgery treatment. The effective heat capacity method is used for simulation of phase change in bio-heat transfer equation to take into account the latent heat of phase transition. The bio-heat transfer equation is solved by using element free Galerkin method (EFGM) to simulate the phase change problem of biological tissues subject to nano cryosurgery. In this study, Murshed model with cylindrical nanoparticles is used for the high thermal conductivity of nanofluids as compared to Leong Model with the spherical nanoparticle. The important effects of the interfacial layer at the mushy region (i.e. liquid to the solid interface), size and concentration of nanoparticles are shown on the freezing process. This type of problem has applications in biomedical treatment such as drug delivery. Application of cryosurgery in bio-fluids used for drug delivery in cancer therapy can be made more efficient in the presence of nanoparticles (such as Iron oxide ($Fe_{3}O_{4}$), alumina ($Al_{2}O_{3}$) and gold ($Au$)).
Cyclisationen I. Darstellung Von Derivaten Des 1.1‐Dimethyl‐Octalins (1957)

Abstract Die säurekatalysierte Cyclisation von p ‐substituierten Myrcen‐Addukten führt zu Verbindungen der 1.1‐Dimethyl‐octalin‐Reihe mit funktionellen Gruppen in 7‐Stellung. Der Einfluß des Cyclisationsmittels und der am Cyclohexenring sitzenden Substituenten auf die Ringbildung wird untersucht. Mit Hilfe von BF 3 werden Ausbeuten von über 90% d. Th. erreicht. Die Eigenschaften der 1.1‐Dimethyl‐octalin‐Derivate werden beschrieben. — Das Verhalten des Myrcens bei der Dien‐Synthese mit unsymmetrisch substituierten Philodienen wird geprüft.
Design, Synthesis, and Properties of a Potent Inhibitor of<i>Pseudomonas aeruginosa</i>Deacetylase LpxC (2017)

Over the past several decades, the frequency of antibacterial resistance in hospitals, including multidrug resistance (MDR) and its association with serious infectious diseases, has increased at alarming rates. Pseudomonas aeruginosa is a leading cause of nosocomial infections, and resistance to virtually all approved antibacterial agents is emerging in this pathogen. To address the need for new agents to treat MDR P. aeruginosa, we focused on inhibiting the first committed step in the biosynthesis of lipid A, the deacetylation of uridyldiphospho-3-O-(R-hydroxydecanoyl)-N-acetylglucosamine by the enzyme LpxC. We approached this through the design, synthesis, and biological evaluation of novel hydroxamic acid LpxC inhibitors, exemplified by 1, where cytotoxicity against mammalian cell lines was reduced, solubility and plasma-protein binding were improved while retaining potent anti-pseudomonal activity in vitro and in vivo.
Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry (2016)

The rapid development of metabolomics has significantly advanced health and disease related research. However, metabolite identification remains a major analytical challenge for untargeted metabolomics. While the use of collision cross-section (CCS) values obtained in ion mobility-mass spectrometry (IM-MS) effectively increases identification confidence of metabolites, it is restricted by the limited number of available CCS values for metabolites. Here, we demonstrated the use of a machine-learning algorithm called support vector regression (SVR) to develop a prediction method that utilized 14 common molecular descriptors to predict CCS values for metabolites. In this work, we first experimentally measured CCS values (Ω<sub>N2</sub>) of ∼400 metabolites in nitrogen buffer gas and used these values as training data to optimize the prediction method. The high prediction precision of this method was externally validated using an independent set of metabolites with a median relative error (MRE) of ∼3%, better than conventional theoretical calculation. Using the SVR based prediction method, a large-scale predicted CCS database was generated for 35 203 metabolites in the Human Metabolome Database (HMDB). For each metabolite, five different ion adducts in positive and negative modes were predicted, accounting for 176 015 CCS values in total. Finally, improved metabolite identification accuracy was demonstrated using real biological samples. Conclusively, our results proved that the SVR based prediction method can accurately predict nitrogen CCS values (Ω<sub>N2</sub>) of metabolites from molecular descriptors and effectively improve identification accuracy and efficiency in untargeted metabolomics. The predicted CCS database, namely, MetCCS, is freely available on the Internet.
Needles in a Haystack: Plan Recognition in Large Spatial Domains Involving Multiple Agents (1998)

While plan recognition research has been applied to a wide variety of problems, it has largely made identical assumptions about the number of agents participating in the plan, the observability of the plan execution process, and the scale of the domain. We describe a method for plan recognition in a real-world domain involving large numbers of agents performing spatial maneuvers in concert under conditions of limited observability. These assumptions differ radically from those traditionally made in plan recognition and produce a problem which combines aspects of the fields of plan recognition, pattern recognition, and object tracking. We describe our initial solution which borrows and builds upon research from each of these areas, employing a pattern-directed approach to recognize individual movements and generalizing these to produce inferences of large-scale behavior. Introduction Plan recognition, the problem of inferring goals, intentions, or future actions given observations of ...
First Direct C-2-Lithiation of 4-DMAP. Convenient Access to Reactive Functional Derivatives and Ligands (2001)

The first direct alpha-lithiation of 4-DMAP has been performed via reaction with the BuLi-Me(2)N(CH(2))(2)OLi (BuLi-LiDMAE) reagent. This new methodology avoids the use of a activation-lithiation-regeneration sequence or halogen-metal exchange classically employed. New useful DMAP-containing synthons and polyheterocycles have been efficiently prepared.
Automatic Power Plants for Telephone Offices (1931)

The nature of power requirements for telephone offices is discussed, with emphasis on continuity of service. Automatic controls are indicated because of their more exact performance, with consequent reduction in variations and in interruptions and their saving in maintenance, particularly with 24-hour operation demanded. Developments are traced, showing an increasing trend toward automatic regulation and control of main power supplies, ringing and other signaling energy sources. The development of ``unit type power plants'' for telephone offices is discussed and information is given on a number of standardized plants which operate upon a full automatic or a semi-automatic basis. These furnish power supply for manual, toll, and telegraph central offices, for magneto offices and for manual and dial system private branch exchanges also for small dial system central offices. Favorable operating experience points the way toward further introduction of automatic devices which will place most telephone power plants, except those in the larger dial system offices, in a position to operate themselves over considerable intervals of time.
Reduced Fouling of Ultrafiltration Membranes Via Surface Fluorination (1993)

Abstract The fouling resistance of a polysulfone membrane can be improved by fluorination. In the filtration of potato waste streams, fluorination of polysulfone membranes has improved both the initial flux and fouling rates of the treated membranes. Selectivities of the membranes as measured by COD and total organic nitrogen rejection were not affected by the fluorination process. The fluorination process adds both fluorine and oxygen to the surface, and the increased oxygen and fluorine on the surface of the membrane increase the hydrophilic nature of the membrane. This increase of hydrophilicity reduces the rate of adsorption of hydrophobic foulants to the surface, decreasing the fouling rate. Increased hydrophilicity also decreases the capillary pressure and permits permeate flow through smaller pores.
VEGF binding to NRP1 is essential for VEGF stimulation of endothelial cell migration, complex formation between NRP1 and VEGFR2, and signaling via FAK Tyr407 phosphorylation (2011)

In endothelial cells, neuropilin-1 (NRP1) binds vascular endothelial growth factor (VEGF)-A and is thought to act as a coreceptor for kinase insert domain-containing receptor (KDR) by associating with KDR and enhancing VEGF signaling. Here we report mutations in the NRP1 b1 domain (Y297A and D320A), which result in complete loss of VEGF binding. Overexpression of Y297A and D320A NRP1 in human umbilical vein endothelial cells reduced high-affinity VEGF binding and migration toward a VEGF gradient, and markedly inhibited VEGF-induced angiogenesis in a coculture cell model. The Y297A NRP1 mutant also disrupted complexation between NRP1 and KDR and decreased VEGF-dependent phosphorylation of focal adhesion kinase at Tyr407, but had little effect on other signaling pathways. Y297A NRP1, however, heterodimerized with wild-type NRP1 and NRP2 indicating that nonbinding NRP1 mutants can act in a dominant-negative manner through formation of NRP1 dimers with reduced binding affinity for VEGF. These findings indicate that VEGF binding to NRP1 has specific effects on endothelial cell signaling and is important for endothelial cell migration and angiogenesis mediated via complex formation between NRP1 and KDR and increased signaling to focal adhesions. Identification of key residues essential for VEGF binding and biological functions provides the basis for a rational design of antagonists of VEGF binding to NRP1.
Effect of the Met344His Mutation on the Conformational Dynamics of Bovine β-1,4-Galactosyltransferase:  Crystal Structure of the Met344His Mutant in Complex with Chitobiose<sup>,</sup><sup>,</sup> (2004)

Beta-1,4-galactosyltransferase (beta4Gal-T1) in the presence of manganese ion transfers galactose from UDP-galactose (UDP-Gal) to N-acetylglucosamine (GlcNAc) that is either free or linked to an oligosaccharide. Crystallographic studies on bovine beta4Gal-T1 have shown that the primary metal binding site is located in the hinge region of a long flexible loop, which upon Mn(2+) and UDP-Gal binding changes from an open to a closed conformation. This conformational change creates an oligosaccharide binding site in the enzyme. Neither UDP nor UDP analogues efficiently induce these conformational changes in the wild-type enzyme, thereby restricting the structural analysis of the acceptor binding site. The binding of Mn(2+) involves an uncommon coordination to the Sdelta atom of Met344; when it is mutated to His, the mutant M344H, in the presence of Mn(2+) and UDP-hexanolamine, readily changes to a closed conformation, facilitating the structural analysis of the enzyme bound with an oligosaccharide acceptor. Although the mutant M344H loses 98% of its Mn(2+)-dependent activity, it exhibits 25% of its activity in the presence of Mg(2+). The crystal structures of M344H-Gal-T1 in complex with either UDP-Gal.Mn(2+) or UDP-Gal.Mg(2+), determined at 2.3 A resolution, show that the mutant enzyme in these complexes is in a closed conformation, and the coordination stereochemistry of Mg(2+) is quite similar to that of Mn(2+). Although either Mn(2+) or Mg(2+), together with UDP-Gal, binds and changes the conformation of the M344H mutant to the closed one, it is the Mg(2+) complex that engages efficiently in catalyses. Thus, this property enabled us to crystallize the M344H mutant for the first time with the acceptor substrate chitobiose in the presence of UDP-hexanolamine and Mn(2+). The crystal structure determined at 2.3 A resolution reveals that the GlcNAc residue at the nonreducing end of chitobiose makes extensive hydrophobic interactions with the highly conserved Tyr286 residue.
New Evidence for Rejuvenation of Phosphorus Retention Capacity in EAF Steel Slag (2008)

The purpose of this research was to investigate phosphorus (P) retention capacity and rejuvenation potential of electric arc furnace (EAF) steel slag from Quebec and New Zealand (NZ) iron melter slag (IMS). Columns filled with slag materials were fed with dairy effluent and subjected to two feeding and one resting cycle(s). P retention capacities and rejuvenation potentials were determined after each feeding cycle. Elemental composition and mineralogical analysis were performed on IMS samples. Finally, chemical fractionation analysis was conducted on both NZ IMS and Quebec EAF steel slags. The results revealed that initiating a resting period in EAF steel slag filters prior to reaching their P saturation point increased the overall filter P retention capacity by 49.5 and 42.4% compared to 28% in a filter which had its resting period initiated after reaching P saturation. The rejuvenation property could play a significant role in full-scale applications by prolonging life expectancy and increasing cost efficiency. P retention and rejuvenation by NZ slag materials was negligible relative to EAF steel slag material from Quebec. Chemical fractionation analysis revealed differences between materials, indicating that the highest quantities of P were bound to Ca and Fe in EAF steel slag and to Ca and Al fractions in iron melter slag. This study also demonstrates that slag's performance is dependent on the source of the material and the steel making practices. Therefore, testing of the P adsorptive capability and, if relevant, the rejuvenation potential of individual steel mill slags, should be a prerequisite prior to their use in field applications.
Feature-level fusion of palmprint and palm vein for person identification based on a &#x201C;Junction Point&#x201D; representation (2008)

The issue of how to represent the palm features for effective classification is still an open problem. In this paper, we propose a novel palm representation, the “Junction Points” (JP) set, which is formed by the two set of line segments extracted from the registered palmprint and palm vein images respectively. Unlike the existing approaches, the JP set, containing position and orientation information, is a more compact feature that significantly reduces the storage requirement. We compare the proposed JP approach with the line-based methods on a large dataset. Experimental results show that the proposed JP approach provides a better representation and achieves lower error rate in palm verification.
CATNAP: a tool to compile, analyze and tally neutralizing antibody panels (2015)

CATNAP (Compile, Analyze and Tally NAb Panels) is a new web server at Los Alamos HIV Database, created to respond to the newest advances in HIV neutralizing antibody research. It is a comprehensive platform focusing on neutralizing antibody potencies in conjunction with viral sequences. CATNAP integrates neutralization and sequence data from published studies, and allows users to analyze that data for each HIV Envelope protein sequence position and each antibody. The tool has multiple data retrieval and analysis options. As input, the user can pick specific antibodies and viruses, choose a panel from a published study, or supply their own data. The output superimposes neutralization panel data, virus epidemiological data, and viral protein sequence alignments on one page, and provides further information and analyses. The user can highlight alignment positions, or select antibody contact residues and view position-specific information from the HIV databases. The tool calculates tallies of amino acids and N-linked glycosylation motifs, counts of antibody-sensitive and -resistant viruses in conjunction with each amino acid or N-glycosylation motif, and performs Fisher's exact test to detect potential positive or negative amino acid associations for the selected antibody. Website name: CATNAP (Compile, Analyze and Tally NAb Panels). Website address: http://hiv.lanl.gov/catnap.
Model analysis for business event processing (2007)

Business event processing requires efficiently processing live events, computing business performance metrics, detecting business situations, and providing real-time visibility of key performance indicators. Given the high volume of events and significant complexity of computation, system performance—event throughput—is critical. In this paper, we advocate model-analysis techniques to improve event throughput. In the build time, a series of model analyses of the application logic are conducted to understand such factors as runtime data-access path, data flow, and control flow. Such analyses can be used to improve throughput three ways: at build time it can be used to facilitate the generation of customized code to optimize I/O and CPU usage; information about the control flow and data flow can be used to ensure that CPU resources are used effectively by distributing event-processing computation logic evenly over time; and at runtime, knowledge gained from the model can be used to plan multithreaded parallel event-processing execution to reduce wait states by maximizing parallelization and reducing the planning overhead. This paper presents a series of model-analysis techniques and the results of experiments that demonstrate their effectiveness.
Attack on a DFA Protected AES by Simultaneous Laser Fault Injections (2016)

This paper demonstrates a Fault Attack on anAES core protected by an infection type countermeasure. The redundant AES is implemented on a Xilinx Spartan-6FPGA, with a feature size of 45 nm. By injecting exactlythe same fault in both state registers of the redundant implementation using lasers, we are able to annul the protection added by the countermeasure and thus perform a successful Differential Fault Analysis. This requires a high precision double laser setup in order to hit two different locations on the chip at the same point intime. With a priori knowledge about the location of bothstate registers, we were able to generate applicable faultyciphertexts within minutes. Our results show that forapplications demanding a high level of security, relyingon a duplication of hardware is not sufficient.
Enhanced and long term immunogenicity of a Her-2/neu multi-epitope vaccine conjugated to the carrier CRM197 in conjunction with the adjuvant Montanide (2017)

Fusion of the B cell peptides has led to additional generation of CD4 T cell epitopes, and this P467-multi epitope vaccine was found to induce polyclonal antibody responses with anti-proliferative capacity against Her-2/neu. The hybrid vaccine together with Montanide induced higher and long-lasting antibody levels, Th1-biased cellular responses being superior to vaccination with the single B cell peptides. This vaccine formulation is now planned to be evaluated in a phase Ib/II study in Her-2/neu overexpressing cancer patients.
The involvement of protein kinase C isoenzymes alpha, epsilon and zeta in the sensitivity to antitumor treatment and apoptosis induction. (2000)

In order to obtain additional information on the involvement of protein kinase C (PKC) isoenzymes in the resistance of cells to anticancer drugs and in the induction of apoptosis, we employed antisense oligonucleotides to PKC alpha and PKC zeta, CGP 53506, a new inhibitor of PKC alpha, and cells overexpressing PKC alpha, PKC epsilon and PKC zeta. We found that in HeLa cells which express PKC alpha and zeta, down-modulation of either PKC alpha or PKC zeta with antisense oligonucleotides induced apoptosis. The PKC alpha selective inhibitor CGP 53506 reduced the proliferation rate of PKC alpha overexpressing NIH3T3 cells more than that of wild-type cells and induced apoptosis, indicating that such a PKC alpha inhibitor may be useful in the treatment of tumors overexpressing PKC alpha such as glioblastomas. NIH3T3 cells overexpressing PKC alpha were more resistant, whereas NIH3T3 cells overexpressing PKC epsilon or PKC zeta were more sensitive to treatment with cis-platin, adriamycin or gamma-irradiation compared to parental NIH3T3 wild-type cells. The observed resistance and sensitization corresponded to the extent of apoptosis induced by these treatments. Alterations in the expression of p53, bcl-2 and bax in the PKC isoenzyme overexpressing cells indicate that these proteins may be involved in the different sensitivities of these cells.