gebhart/patrepeval huggingface dataset:
Uric Acid Causes Vascular Smooth Muscle Cell Proliferation by Entering Cells via a Functional Urate Transporter (2005)

Urate enters VSMC by both voltage-sensitive and OAT pathways, and the uptake, cell proliferation and MCP-1 expression can be blocked by OAT inhibitors. The specific transporter(s) responsible for the urate uptake remains to be determined.
The synthesis of alternating alpha,beta-oligodeoxyribonucleotides with alternating (3'-->3')- and (5'-->5')-internucleotic linkages as potential therapeutic agents. (1993)

A simplified synthesis of alpha-2'-deoxyribonucleoside derivatives has been developed and the solid-phase preparation of antisense alpha,beta-oligodeoxyribonucleotides with alternating (3'-->3')- and (5'-->5')-internucleotidic phosphodiester linkages, targeted against HIV-1 tat mRNA, has been accomplished. Hybridization properties of these oligonucleotide analogues have been investigated.
A fluoride-catalyzed sol–gel route to catalytically active non-ordered mesoporous silica materials in the absence of surfactants (2005)

A fluoride catalyzed route for the synthesis of catalytically active non-ordered mesoporous silica based materials in the absence of surfactants is presented and discussed. This synthesis procedure has allowed the introduction of different organic and inorganic functionalities with specific chemical activities within silica networks with well-tailored mesoporous distributions. Particularly, this sol–gel synthesis route has permitted the synthesis of Al- and Ti-containing mesoporous silica materials that have been found to be catalytically active for acid and redox processes, respectively. This synthetic approach has also allowed the preparation of hybrid organic–inorganic mesoporous materials.
Blood flow reductions in stenosed canine coronary arteries: vasospasm or platelet aggregation? (1982)

In 67 dogs with a 60-80% coronary stenosis produced by an external constricting plastic ring, blood flow measured with an electromagnetic flowmeter showed cyclical flow reductions of varying magnitude and duration, and then an abrupt return to control flow. In 45 dogs, heparin did not prevent these flow reductions, but ibuprofen (Motrin) or indomethacin abolished them. With incremental doses of each of these drugs, the cyclical flow reduction and the platelet function in vitro were diminished proportionately. In 10 more dogs, during low flow, pinching or poking the narrowed vessel suddenly restored normal flow. Topical application of papaverine and nitroglycerin proximal to the stenosis did not abolish the cyclic flow reduction, although a transient fall in systemic pressure indicated that they had been absorbed. Seven dogs had the constricting cylinder and flow probe chronically implanted for 4-6 weeks. A single oral dose of aspirin, 20 mg/kg, abolished their cyclic flow reductions for 2-4 days. In five dogs with 70% stenosis in the circumflex coronary artery, coronary arteriography was performed before coronary flow reduction and when coronary blood flow was low. This showed that there was a considerable additional reduction in the size of the mechanically constricted lumen during spontaneous flow reduction. In one dog, a nonopacified mass was dislodged from the area of constriction in 67 msec and this restored the lumen to its control diameter. Similar rapid clearing was filmed in two more dogs. In no case was vasospasm observed. These results suggest that obstruction from platelets aggregated in the narrowed lumen caused the cyclic flow reductions.
Early studies on DNA-based immunizations for measles virus (1997)

DNA-mediated immunizations have been used to raise neutralizing antibodies for measles virus. Single inoculations of plasmids expressing measles hemagglutinin or fusion glycoproteins raised neutralizing antibody in BALB/c mice. Plasmids expressing the hemagglutinin glycoprotein (both normal and secreted) raised neutralizing responses that persisted for 1 year. For both forms of hemagglutinin, the effectiveness of the raised antibody (ratio of neutralizing activity to ELISA activity) was similar. High titers of neutralizing antibody were also raised by inoculation of rabbits with the hemagglutinin and fusion glycoprotein-expressing plasmids.
T cell activation, from atopy to asthma: more a paradox than a paradigm (2003)

During the last 15 years, it was largely shown that allergic inflammation was orchestrated by activated Th2 lymphocytes, leading to IgE production and eosinophil activation. Indeed, Th2 activation was shown to be necessary to induce allergic sensitization in animal models. In humans, a Th2 skewing was shown in atopic children soon after birth. In asthma, descriptive studies showed that Th2 cells were more numerous in patients than in controls. In addition, during specific allergen stimulation, an increase of Th2 cells was described in most cases. According to this Th2 paradigm, it was proposed that early avoidance of microbial exposure could explain the increase of atopic diseases seen in the last 20 years in developed countries, as the "hygiene hypothesis". Recently, it was proposed that early exposure to lipopolysaccharide (LPS) could be protective against atopic diseases. However, it is well established that exposure to LPS can induce asthma symptoms, both in animals and humans, although it induces a Th1 inflammatory response. In addition, most infections induce asthma exacerbations and Th1 responses. Recently, some studies have showed that some Th1 cells were present in asthmatic patients, which could be related to bronchial hyperreactivity. There is therefore an "infectious paradox" in asthma, which contributes to show that the Th2 paradigm is insufficient to explain the whole inflammatory reaction of this disease. We propose that the Th2paradigm is relevant to atopy and inception of asthma albeit a Th1 activation would account at least in part for bronchial hyperreactivity and asthma symptoms.
Algorithm of Particle Data Association for SLAM Based on Improved Ant Algorithm (2014)

&lt;p&gt;The article considers a problem of data association algorithm for simultaneous localization and mapping guidelines in determining the route of unmanned aerial vehicles (UAVs). Currently, these equipments are already widely used, but mainly controlled from the remote operator. An urgent task is to develop a control system that allows for autonomous flight. Algorithm SLAM (simultaneous localization and mapping), which allows to predict the location, speed, the ratio of flight parameters and the coordinates of landmarks and obstacles in an unknown environment, is one of the key technologies to achieve real autonomous UAV flight. The aim of this work is to study the possibility of solving this problem by using an improved ant algorithm.&lt;/p&gt;&lt;p&gt;The data association for SLAM algorithm is meant to establish a matching set of observed landmarks and landmarks in the state vector. Ant algorithm is one of the widely used optimization algorithms with positive feedback and the ability to search in parallel, so the algorithm is suitable for solving the problem of data association for SLAM. But the traditional ant algorithm in the process of finding routes easily falls into local optimum. Adding random perturbations in the process of updating the global pheromone to avoid local optima. Setting limits pheromone on the route can increase the search space with a reasonable amount of calculations for finding the optimal route.&lt;/p&gt;&lt;p&gt;The paper proposes an algorithm of the local data association for SLAM algorithm based on an improved ant algorithm. To increase the speed of calculation, local data association is used instead of the global data association. The first stage of the algorithm defines targets in the matching space and the observed landmarks with the possibility of association by the criterion of individual compatibility (IC). The second stage defines the matched landmarks and their coordinates using improved ant algorithm. Simulation results confirm the efficiency and effectiveness of the algorithm.&lt;/p&gt;
A novel approach to developer-soluble anti-reflective coatings for 248-nm lithography (2007)

A novel approach to developer-soluble bottom anti-reflective coatings (BARCs) for 248-nm lithography was demonstrated. The BARC formulations are photosensitive, dye-filled systems incorporated with a polymer binder. The films are generated by thermally crosslinking the polymer matrix, and are then photochemically decrosslinked in order to render them soluble in developer solutions. The BARCs are compatible with solvents commonly used in the industry. Easy modification of the films with regard to optical properties for potential use with various substrates was also demonstrated. The BARCs exhibit anisotropic development in aqueous tetramethylammonium hydroxide (TMAH) solutions subsequent to simulated photoresist application, exposure, and post-exposure bake.
An Efficient Method of Selectable Marker Gene Excision by Xer Recombination for Gene Replacement in Bacterial Chromosomes (2006)

A simple, effective method of unlabeled, stable gene insertion into bacterial chromosomes has been developed. This utilizes an insertion cassette consisting of an antibiotic resistance gene flanked by dif sites and regions homologous to the chromosomal target locus. dif is the recognition sequence for the native Xer site-specific recombinases responsible for chromosome and plasmid dimer resolution: XerC/XerD in Escherichia coli and RipX/CodV in Bacillus subtilis. Following integration of the insertion cassette into the chromosomal target locus by homologous recombination, these recombinases act to resolve the two directly repeated dif sites to a single site, thus excising the antibiotic resistance gene. Previous approaches have required the inclusion of exogenous site-specific recombinases or transposases in trans; our strategy demonstrates that this is unnecessary, since an effective recombination system is already present in bacteria. The high recombination frequency makes the inclusion of a counter-selectable marker gene unnecessary.
Heteroepitaxial Growth of CeO2(001) Films on Si(001) Substrates by Pulsed Laser Deposition in Ultrahigh Vacuum (1991)

Pulsed laser deposition in ultrahigh vacuum (UHV) was applied to the epitaxial growth of CeO 2 film on Si(001). Although the direct deposition of CeO 2 (001) on Si(001) was unsuccessful, the desired epitaxy was achieved by inserting the growth of a SrTiO 3 layer. The formation of a CeO 2 (001)//SrTiO 3 (001)//Si(001) layered structure was verified by reflection high-energy electron diffraction analysis of the growing surface at a temperature between 650 and 700°C in UHV. In addition to lattice matching, chemical interaction at the growing surface had a decisive effect on the epitaxy and orientation of growing ceramic lattices.
Integrating metabolism and toxicity in multi-organ systems. (2001)

A wide range of experimental and predictive approaches are currently employed by the pharmaceutical industry in an attempt to avoid developing molecules with likely toxicities. Experimental systems may be adapted to handle the increasing number of molecules that require screening. The cost implication of such extensive screening is, however, immense and in silico models must therefore become the first lines of investigation to assess the metabolic and toxicological potential of new compound libraries. In silico systems have been based on the relationship between the chemical structure of novel molecules and toxicological outcomes in terms of types, but not always, locations of lesions. There should be sufficient published and in-house data available on the distribution of diverse molecules to identify the rules that govern organ, cellular and subcellular distribution of molecules (and their metabolites) as the basis of tissue and cell targeting and, more importantly, the possibility of toxicological processes. In addition, the extensive cell biology knowledge needs to be linked to current in silico systems to enhance our understanding of metabolic activation and other processes that affect likely toxicological consequences in different tissues and specific cell types. There is a need to provide a single knowledge platform that can access all current in silico products that use different datasets. The closer integration of these diverse tools will help predict other approaches to help identify the most likely toxicological potential of novel molecules, and ensure the 'least' toxic molecules are developed.
Phage antibodies with pan-species recognition of the oncofoetal angiogenesis marker fibronectin ED-B domain (1996)

Fibronectin (FN) exists in several polymorphic forms due to alternative splicing. The B-FN isoform (with ED-B domain inserted by splicing) is present in the stroma of foetal and neoplastic tissues and in adult and neoplastic blood vessels during angiogenesis but is undetectable in mature vessels. This isoform, therefore, represents a promising marker for angiogenesis, as already shown using the mouse monoclonal antibody (MAb) BC-1 directed against an epitope on human B-FN. However, this MAb does not directly recognise the human ED-B domain nor does it recognise B-FN of other species; therefore, it cannot be used as a marker of angiogenesis in animal models. In principle, antibodies directed against the human ED-B domain should provide pan-species markers for angiogenesis as the sequence of this domain is highly conserved in different species (and identical in humans and mice). As it has proved difficult to obtain such antibodies by hybridoma technology, we used phage display technology. Here, we describe the isolation of human antibody fragments against the human ED-B domain that bind to human, mouse and chicken B-FN. As shown by immunohistochemistry, the antibody fragments stain human neoplastic tissues and the human, mouse and chicken neovasculature.
Conservation Voltage Reduction (CVR) at Northeast Utilities (1987)

This paper presents the results of field tests conducted on the Northeast Utilities (NU) distribution system to measure changes in energy consumption resulting from voltage reduction. The economics of achieving a permanent voltage reduction by compressing existing state voltage limits to a narrower band is also examined. Although the field tests indicate that there are energy savings associated with voltage reduction, it is uneconomical to achieve voltage reduction on the NU system by compressing existing voltage limits. The use of existing line drop compensation controls is identified as a practical method of achieving voltage reduction without changing existing voltage limits.
ChemInform Abstract: Rhodium‐Catalyzed Formylation of Organomercurials: Application to Efficient Polyol Synthesis. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Impact of Genomics on Drug Discovery (2000)

High-throughput gene sequencing has revolutionized the process used to identify novel molecular targets for drug discovery. Thousands of new gene sequences have been generated but only a limited number of these can be converted into validated targets likely to be involved in disease. We describe here some of the approaches used at SmithKline Beecham to select and validate novel targets. These include the identification of selective tissue gene product expression, such as for cathepsin K, a novel osteoclast-specific cysteine protease. We also describe the discovery and functional characterization of novel members of the G-protein coupled receptor superfamily and their pairing with natural ligands. Lastly, we discuss the promises of gene microarrays and proteomics, developing technologies that allow the parallel analyses of tissue expression patterns of thousands of genes or proteins, respectively.
Antiemesis (2012)

Chemotherapy-induced (or radiotherapy-induced) vomiting (emesis) and nausea can significantly affect a patient's quality of life, leading to poor compliance with further chemotherapy or radiation therapy treatment. ]
Lysosome-mediated processing of chromatin in senescence (2013)

Cellular senescence is a stable proliferation arrest, a potent tumor suppressor mechanism, and a likely contributor to tissue aging. Cellular senescence involves extensive cellular remodeling, including of chromatin structure. Autophagy and lysosomes are important for recycling of cellular constituents and cell remodeling. Here we show that an autophagy/lysosomal pathway processes chromatin in senescent cells. In senescent cells, lamin A/C-negative, but strongly γ-H2AX-positive and H3K27me3-positive, cytoplasmic chromatin fragments (CCFs) budded off nuclei, and this was associated with lamin B1 down-regulation and the loss of nuclear envelope integrity. In the cytoplasm, CCFs were targeted by the autophagy machinery. Senescent cells exhibited markers of lysosomal-mediated proteolytic processing of histones and were progressively depleted of total histone content in a lysosome-dependent manner. In vivo, depletion of histones correlated with nevus maturation, an established histopathologic parameter associated with proliferation arrest and clinical benignancy. We conclude that senescent cells process their chromatin via an autophagy/lysosomal pathway and that this might contribute to stability of senescence and tumor suppression.
N-ethylmaleimide-sensitive fusion protein: a trimeric ATPase whose hydrolysis of ATP is required for membrane fusion. (1994)

The NEM-sensitive fusion protein, NSF, together with SNAPs (soluble NSF attachment proteins) and the SNAREs (SNAP receptors), is thought to be generally used for the fusion of transport vesicles to their target membranes. NSF is a homotrimer whose polypeptide subunits are made up of three distinct domains: an amino-terminal domain (N) and two homologous ATP-binding domains (D1 and D2). Mutants of NSF were produced in which either the order or composition of the three domains were altered. These mutants could not support intra-Golgi transport, but they indicated that the D2 domain was required for trimerization of the NSF subunits. Mutations of the first ATP-binding site that affected either the binding (K266A) or hydrolysis (E329Q) of ATP completely eliminated NSF activity. The hydrolysis mutant was an effective, reversible inhibitor of Golgi transport with an IC50 of 125 ng/50 microliters assay. Mutants in the second ATP-binding site (binding, K549A; hydrolysis, D604Q) had either 14 or 42% the specific activity of the wild-type protein, respectively. Using coexpression of an inactive mutant with wild-type subunits, it was possible to produce a recombinant form of trimeric NSF that contained a mixture of subunits. The mixed NSF trimers were inactive, even when only one mutant subunit was present, suggesting that NSF action requires each of the three subunits in a concerted mechanism. These studies demonstrate that the ability of the D1 domain to hydrolyze ATP is required for NSF activity and, therefore is required for membrane fusion. The D2 domain is required for trimerization, but its ability to hydrolyze ATP is not absolutely required for NSF function.
Classical complement pathway activation on nucleated cells. Role of factor H in the control of deposited C3b (1995)

The restriction of alternative complement pathway activation in fluid phase or on nonactivator surfaces has been described as the major physiologic function of the complement regulatory protein factor H. In this study, we provide evidence that factor H is also a restriction factor of classical pathway activation on the surface of nucleated cells. We found that C3b was rapidly converted to inactivated C3b (iC3b) on human SK-MEL-93-2 melanoma cells after classical pathway activation with the murine monoclonal IgG3 Ab R24 directed against the disialoganglioside surface Ag GD3. The SK-MEL-93-2 cells are nonactivators of the alternative pathway and express neither CR1 (CD35) nor the C3b-cleaving protease p65. The cells are further characterized by the expression of only moderate amounts of DAF (CD55) and approximately 5 x 10(3) MCP (CD46) molecules/cell. FACS analysis and direct quantitation using [125I]factor H revealed high level binding of factor H to the melanoma cells (5.6 x 10(6) molecules/cell) during classical pathway activation. The binding of factor H could be inhibited under conditions that inactivate the classical complement pathway (EGTA and heat treatment), but not by factor B depletion of the serum, demonstrating that classical pathway activation was responsible for factor H binding. Treatment of factor B-depleted serum with neutralizing concentrations of polyclonal anti-factor H resulted in the prolonged presence of intact C3b on the cells and a significantly reduced generation of iC3b. The increased amount of C3b on these cells correlated with a 2.65-fold greater rate of cell death. In contrast, the increase in cell death effected by neutralizing concentrations of anti-CD46 or anti-CD55 Ab was only 0.13- or 0.35-fold, respectively. In addition, the supplementation of serum with purified factor H decreased the extent of lysis of the cells. Collectively, these data provide experimental evidence that factor H, through its cofactor activity for C3b degradation, is involved in the restriction of the classical pathway of complement on the surface of nucleated cells, a function that to date has been exclusively attributed to the membrane regulatory proteins CD35 and CD46.
Computationally Optimised DNA Assembly of synthetic genes (2008)

Gene synthesis is hampered by two obstacles: improper assembly of oligonucleotides; oligonucleotide defects incurred during chemical synthesis. To overcome the first problem, we describe the employment of a Computationally Optimised DNA Assembly (CODA) algorithm that uses the degeneracy of the genetic code to design overlapping oligonucleotides with thermodynamic properties for self-assembly into a single, linear, DNA product. To address the second problem, we describe a hierarchical assembly strategy that reduces the incorporation of defective oligonucleotides into full-length gene constructs. The CODA algorithm and these biological methods enable fast, simple and reliable assemblies of sequence-correct full-length genes.