gebhart/patrepeval huggingface dataset:
Monoclonal antibodies as probes of the distribution of ZP-2, the major sulfated glycoprotein of the murine zona pellucida. (1984)

Three sulfated glycoproteins (ZP-1, ZP-2, and ZP-3) make up the zona pellucida, an extracellular glycocalyx that surrounds mouse oocytes. We have produced five monoclonal antibodies specific to the zona. All five immunoprecipitated ZP-2, and in addition, two of the antibodies immunoprecipitated ZP-3. This suggests the presence of either a common antigenic site or one made up in part by each of the two glycoproteins. The monoclonal antibodies bound to approximately 1.3 X 10(8) binding sites per ovulated mouse egg which represents 2% of the total number of ZP-2 molecules present in the zona. ZP-2 appeared to be present throughout the zona and indirect immunofluorescence revealed a fibrous pattern with no evidence of localization. Furthermore, this pattern of distribution, which was identical for all five monoclones, remained constant after fertilization at the two-cell embryo stage. Laser photobleaching demonstrated that ZP-2 is stably integrated in the extracellular matrix of the zona pellucida. No mouse tissue other than the ovary contained ZP-2 and ZP-2 is antigenically distinct from other previously described extracellular matrix proteins.
The UCSF-FDA TransPortal: A Public Drug Transporter Database (2012)

Drug transporters play a key role in the absorption, distribution, and elimination of many drugs, and they appear to be important determinants of therapeutic and adverse drug activities. Although a large body of data pertaining to drug transporters is available, there are few databases that inform drug developers, regulatory agencies, and academic scientists about transporters that are important in drug action and disposition. In this article, we inform the scientific community about the UCSF-FDA TransPortal, a new and valuable online resource for research and drug development.
RNAhybrid: microRNA target prediction easy, fast and flexible (2006)

In the elucidation of the microRNA regulatory network, knowledge of potential targets is of highest importance. Among existing target prediction methods, RNAhybrid [M. Rehmsmeier, P. Steffen, M. Höchsmann and R. Giegerich (2004) RNA, 10, 1507-1517] is unique in offering a flexible online prediction. Recently, some useful features have been added, among these the possibility to disallow G:U base pairs in the seed region, and a seed-match speed-up, which accelerates the program by a factor of 8. In addition, the program can now be used as a webservice for remote calls from user-implemented programs. We demonstrate RNAhybrid's flexibility with the prediction of a non-canonical target site for Caenorhabditis elegans miR-241 in the 3'-untranslated region of lin-39. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid.
Fever in the critically ill medical patient (2009)

Fever, commonly defined by a temperature of >or=38.3 degrees C (101 degrees F), occurs in approximately one half of patients admitted to intensive care units. Fever may be attributed to both infectious and noninfectious causes, and its development in critically ill adult medical patients is associated with an increased risk for death. Although it is widespread and clinically accepted practice to therapeutically lower temperature in patients with hyperthermic syndromes, patients with marked hyperpyrexia, and selected populations such as those with neurologic impairment, it is controversial whether most medical patients with moderate degrees of fever should be treated with antipyretic or direct cooling therapies. Although treatment of fever may improve patient comfort and reduce metabolic demand, fever is a normal adaptive response to infection and its suppression is potentially harmful. Clinical trials specifically comparing fever management strategies in neurologically intact critically ill medical patients are needed.
Insertional Mutagenesis of the Drosophila Genome with Single P Elements (1988)

A versatile genetic method for identifying and cloning Drosophila melanogaster genes affecting any recognizable phenotype is described. Strains are constructed in which the insertion of a single P transposable element has caused a new mutation, greatly simplifying the genetic and molecular analysis of the affected gene. Mutagenesis is initiated by crossing two strains, each of which contains a specially designed P element. One element (jumpstarter), encoding P element transposase, efficiently mobilizes the second nonautonomous transposon (mutator), whose structure facilitates selection and cloning of new insertion mutations. Random mutator transpositions are captured in individual stocks that no longer contain jumpstarter, where they remain stable. This method was used to construct 1300 single P element insertion stocks which were then screened for recessive mutations. A library of single-element insertion strains will allow the structure and function of Drosophila genes to be readily correlated, and should have many other applications in Drosophila molecular genetics.
The sensing contact lens. (2006)

A novel contact lens with embedded sensors is being developed for continuous monitoring of the intraocular pressure in glaucoma patients. Its mode of operation and capabilities are described.
General Synthesis of Periodic Macroporous Solids by Templated Salt Precipitation and Chemical Conversion (2000)

This paper presents a general method to prepare three-dimensionally ordered macroporous (3DOM) metal oxides or carbonates via templating with polystyrene (PS) spheres. The method is based on templated precipitation of metal salts (acetates, oxalates, oxides) within a colloidal crystal of PS spheres and subsequent chemical conversion of the inorganic precursors. The compositional range of possible macroporous products includes oxides or carbonates of many metals in the periodic table (e.g., MgO, Cr2O3, Mn2O3, Fe2O3, Co3O4, NiO, ZnO, CaCO3), including compositions that are less accessible or more expensive by previous syntheses based on metal alkoxide precursors. Optimal synthesis conditions and structural features of selected materials are described, on the basis of XRD, TGA, SEM, TEM, nitrogen adsorption data, and chemical analysis.
MicC, a Second Small-RNA Regulator of Omp Protein Expression inEscherichia coli (2004)

In a previous bioinformatics-based search for novel small-RNA genes encoded by the Escherichia coli genome, we identified a region, IS063, located between the ompN and ydbK genes, that encodes an approximately 100-nucleotide small-RNA transcript. Here we show that the expression of this small RNA is increased at a low temperature and in minimal medium. Twenty-two nucleotides at the 5' end of this transcript have the potential to form base pairs with the leader sequence of the mRNA encoding the outer membrane protein OmpC. The deletion of IS063 increased the expression of an ompC-luc translational fusion 1.5- to 2-fold, and a 10-fold overexpression of the small RNA led to a 2- to 3-fold repression of the fusion. Deletion and overexpression of the IS063 RNA also resulted in increases and decreases, respectively, in OmpC protein levels. Taken together, these results suggest that IS063 is a regulator of OmpC expression; thus, the small RNA has been renamed MicC. The antisense regulation was further demonstrated by the finding that micC mutations were suppressed by compensatory mutations in the ompC mRNA. MicC was also shown to inhibit ribosome binding to the ompC mRNA leader in vitro and to require the Hfq RNA chaperone for its function. We suggest that the MicF and MicC RNAs act in conjunction with the EnvZ-OmpR two-component system to control the OmpF/OmpC protein ratio in response to a variety of environmental stimuli.
Transcutaneous electrical nerve stimulation and conditioned pain modulation influence the perception of pain in humans (2013)

TENS application increases PPT; however, combining CPM and TENS does not increase the CPM's hypoalgesic response. CPM effect on PPT is associated with the effects of TENS on PPT.
The basophil activation marker defined by antibody 97A6 is identical to the ectonucleotide pyrophosphatase/phosphodiesterase 3 (2001)

It has recently been shown that monoclonal antibody (MoAb) 97A6 detects a surface antigen expressed on basophils and their CD34(+) precursor cells, as well as the basophil cell line KU-812. In this report the partial amino acid sequence of affinity chromatography- and sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated 97A6 antigen(s) from KU-812 lysates was determined. Sequence alignment of high-performance liquid chromatography-selected tryptic peptides from the resulting 130- and 150-kd bands revealed a 100% identity with amino acids 393 to 405 of ectonucleotide pyrophosphatase/phosphodiesterase-3 (E-NPP3; CD203c) but not of the related ectoenzyme PC-1 (E-NPP1). Moreover, MoAb 97A6 selectively recognized 293 cells transfected with human E-NPP3, but did not react with cells transfected with PC-1 or parental 293 cells. In addition, E-NPP3 messenger RNA expression was detected in basophils but not other peripheral blood cells. Finally, MoAb 97A6 immunoprecipitated phosphodiesterase activity from KU-812 cells and peripheral blood basophils, but not from other cell populations. These data demonstrate that MoAb 97A6 recognizes the functionally active type II transmembrane ectoenzyme E-NPP3.
Adherence of coagulase‐negative staphylococci to heparin and other glycosaminoglycans immobilized on polymer surfaces (1994)

The adherence of clinical isolates of staphylococci to surfaces immobilized with various glycosaminoglycans (GAGs) was studied. In general, cells of strains of coagulase-negative (CNS) staphylococci showed a greater adherence to polyethylene surfaces than did cells of Staphylococcus aureus, as studied by bioluminescence. When the surface was heparinized, the adherence of staphylococcal cells decreased, but CNS cells still adhered in greater numbers than did cells of S. aureus. The adherence of CNS to serum-coated heparinized surfaces was of the same magnitude, or increased compared with nonheparinized surfaces. When the surfaces were preadsorbed with different proteins with known heparin-binding domains, i.e., vitronectin, fibronectin, laminin, or collagen, the S. epidermidis cells showed higher binding to heparinized surfaces than to nonheparinized ones, and also in greater numbers than did other staphylococcal cells. Different CNS strains showed a greater ability to agglutinate polystyrene beads immobilized with heparin than did S. aureus. The adherence of S. epidermidis strain 3380 to polyethylene coated with various GAGs such as heparin and chondroitin, dextran, dermatan, and heparan sulfate was shown to be pH-dependent, with the highest adherence at pH 7.2. This may indicate that CNS have the ability to bind to other domains of host proteins when they are adsorbed to heparinized surfaces, versus to nonheparinized ones.
Holographic grating with two spatial frequencies for the simultaneous study of two spectral profiles (1992)

A dispersive device that permits us to analyze two arbitrary spectral profiles simultaneously with the same detector like an optical multichannel analyzer has been designed. The device consists of a holographic grating with two different spatial frequencies, which are not recorded simultaneously, and that are calculated specifically for two spectral lines under study.
A new technique for reversible permeabilization of live cells for intracellular delivery of quantum dots (2013)

A major challenge with the use of quantum dots (QDs) for cellular imaging and biomolecular delivery is the attainment of QDs freely dispersed inside the cells. Conventional methods such as endocytosis, lipids based delivery and electroporation are associated with delivery of QDs in vesicles and/or as aggregates that are not monodispersed. In this study, we demonstrate a new technique for reversible permeabilization of cells to enable the introduction of freely dispersed QDs within the cytoplasm. Our approach combines osmosis driven fluid transport into cells achieved by creating a hypotonic environment and reversible permeabilization using low concentrations of cell permeabilization agents like Saponin. Our results confirm that highly efficient endocytosis-free intracellular delivery of QDs can be accomplished using this method. The best results were obtained when the cells were treated with 50 μg ml⁻¹ Saponin in a hypotonic buffer at a 3:2 physiological buffer:DI water ratio for 5 min at 4 °C.
Current Management Status of Mercury Emissions from Coal Combustion Facilities (2008)

Mercury (Hg), which is mainly emitted from coal-fired power plants, remains one of the most toxic compounds to both humans and ecosystems. Hg pollution is not a local or regional issue, but a global issue. Hg compounds emitted from anthropogenic sources such as coal-fired power plants, incinerators, and boilers, can be transported over long distances. Since the last decade, many European countries, Canada, and especially the United States, have focused on technology to control Hg emissions. Korea has also recently showed an interest in managing Hg pollution from various combustion sources. Previous studies indicate that coal-fired power plants are one of the major sources of Hg in Korea. However, lack of Hg emission data and feasible emission controls have been major obstacles in Hg study. In order to achieve effective Hg control, understanding the characteristics of current Hg sampling methods and control technologies is essential. There is no one proven technology that fits all Hg emission sources, because Hg emission and control efficiency depend on fuel type, configuration of air pollution control devices, flue gas composition, among others. Therefore, a broad knowledge of Hg sampling and control technologies is necessary to select the most suitable method for each Hg-emitting source. In this paper, various Hg sampling methods, including wet chemistry, dry sorbents trap, field, and laboratory demonstrated control technologies, and international regulations, are introduced, with a focus on coal-fired power plants.
A survey regarding wireless communication standards intended for a high-speed vehicle environment (2007)

The high velocities and dynamic conditions that a vehicular environment represents introduce new and demanding challenges in the area of wireless communication. Vehicle Alert System (VAS) is a research project at Halmstad University, Sweden, focusing on reliable wireless vehicle communication. Typical examples of applications for a vehicle alert system are pre-crash warning, communicating slippery road conditions, emergency vehicle routing etc. In VAS a set of application scenarios have been chosen specifically to illustrate as many interesting research aspects of a vehicle alert system as possible. The chosen scenarios include both vehicle-to-vehicle and vehicle-to-infrastructure communications. Research is conducted on all layers of the communication stack relevant for a vehicle alert system – application, network, data link and the physical layer. From a communication perspective a vehicle alert system is characterized by short event-driven control messages that have to be received without errors in time. This implies that different coding strategies, diversity and retransmission schemes must be used to achieve correctness and robustness against the impairments of the wireless channel.
Homology Modeling and Molecular Dynamics Simulations of the Mu Opioid Receptor in a Membrane–Aqueous System (2005)

Three types of opioid receptors-mu, delta, and kappa-belong to the rhodopsin subfamily in the G protein-coupled receptor superfamily. With the recent characterization of the high-resolution X-ray crystal structure of bovine rhodopsin, considerable attention has been focused on molecular modeling of these transmembrane proteins. In this study, a homology model of the mu opioid receptor was constructed based on the X-ray crystal structure of bovine rhodopsin. A phospholipid bilayer was built around the receptor, and two water layers were placed on both surfaces of the lipid bilayer. Molecular-dynamics simulations were carried out by using CHARMM for the entire system, which consisted of 316 amino acid residues, 92 phospholipid molecules, 8327 water molecules, and 11 chloride counter ions-40 931 atoms altogether. The whole system was equilibrated for 250 ps followed by another 2 ns dynamic simulation. The opioid ligand naltrexone was docked into the optimized model, and the critical amino acid residues for binding were identified. The mu opioid receptor homology model optimized in a complete membrane-aqueous system should provide a good starting point for further characterization of the binding modes for opioid ligands. Furthermore, the method developed herein will be applicable to molecular model building to other opioid receptors as well as other GPCRs.
Rapide: A language and toolset for simulation of distributed systems by partial orderings of events (1997)

This paper describes the Rapide concepts of system architecture, causal event simulation, and some of the tools for viewing and analysis of causal event simulations. Illustration of the language and tools is given by a detailed small example. 1 Introduction Rapide-1.0 [LKA + 95],[LV95] is a computer language for defining and executing models of system architectures. The result of executing a Rapide model is a set of events that occurred during the execution together with causal and timing relationships between events. The production of causal history as a simulation result is, at present, unique to Rapide among event-based languages. Sets of events with causal histories are called posets (partially ordered event sets). 1 Simulators that produce posets provide many new opportunities for analysis of models of distributed and concurrent systems. Rapide-1.0 is structured as a set of languages consisting of the Types, Patterns, Architecture, Constraint, and Executable Module languages...
Synthetic lethal targeting of PTEN mutant cells with PARP inhibitors (2009)

The tumour suppressor gene, phosphatase and tensin homolog (PTEN), is one of the most commonly mutated genes in human cancers. Recent evidence suggests that PTEN is important for the maintenance of genome stability. Here, we show that PTEN deficiency causes a homologous recombination (HR) defect in human tumour cells. The HR deficiency caused by PTEN deficiency, sensitizes tumour cells to potent inhibitors of the DNA repair enzyme poly(ADP-ribose) polymerase (PARP), both in vitro and in vivo. PARP inhibitors are now showing considerable promise in the clinic, specifically in patients with mutations in either of the breast cancer susceptibility genes BRCA1 or BRCA2. The data we present here now suggests that the clinical assessment of PARP inhibitors should be extended beyond those with BRCA mutations to a larger group of patients with PTEN mutant tumours.
CloneCloud (2011)

Mobile applications are becoming increasingly ubiquitous and provide ever richer functionality on mobile devices. At the same time, such devices often enjoy strong connectivity with more powerful machines ranging from laptops and desktops to commercial clouds. This paper presents the design and implementation of CloneCloud, a system that automatically transforms mobile applications to benefit from the cloud. The system is a flexible application partitioner and execution runtime that enables unmodified mobile applications running in an application-level virtual machine to seamlessly off-load part of their execution from mobile devices onto device clones operating in a computational cloud. CloneCloud uses a combination of static analysis and dynamic profiling to partition applications automatically at a fine granularity while optimizing execution time and energy use for a target computation and communication environment. At runtime, the application partitioning is effected by migrating a thread from the mobile device at a chosen point to the clone in the cloud, executing there for the remainder of the partition, and re-integrating the migrated thread back to the mobile device. Our evaluation shows that CloneCloud can adapt application partitioning to different environments, and can help some applications achieve as much as a 20x execution speed-up and a 20-fold decrease of energy spent on the mobile device.
EZN-2208 (PEG-SN38) Overcomes ABCG2-Mediated Topotecan Resistance in BRCA1-Deficient Mouse Mammary Tumors (2012)

BRCA1 dysfunction in hereditary breast cancer causes defective homology-directed DNA repair and sensitivity towards DNA damaging agents like the clinically used topoisomerase I inhibitors topotecan and irinotecan. Using our conditional K14cre;Brca1(F/F);p53(F/F) mouse model, we showed previously that BRCA1;p53-deficient mammary tumors initially respond to topotecan, but frequently acquire resistance by overexpression of the efflux transporter ABCG2. Here, we tested the pegylated SN38 compound EZN-2208 as a novel approach to treat BRCA1-mutated tumors that express ABCG2. We found that EZN-2208 therapy resulted in more pronounced and durable responses of ABCG2-positive tumors than topotecan or irinotecan therapy. We also evaluated tumor-specific ABCG2 inhibition by Ko143 in Abcg2(-/-) host animals that carried tumors with topotecan-induced ABCG2 expression. Addition of Ko143 moderately increased overall survival of these animals, but did not yield tumor responses like those seen after EZN-2208 therapy. Our results suggest that pegylation of Top1 inhibitors may be a useful strategy to circumvent efflux transporter-mediated resistance and to improve their efficacy in the clinic.
Functional Analysis of Domains II, Ib, and III of Pseudomonas exotoxin (1989)

Pseudomonas exotoxin is composed of three structural domains that are responsible for cell recognition, membrane translocation, and ADP-ribosylation. The substitution of the cell recognition domain (domain Ia) with a growth factor such as transforming growth factor alpha (TGF alpha), creates a cell-specific cytotoxic agent, TGF alpha-PE40, which kills cells bearing epidermal growth factor (EGF) receptors. We have used TGF alpha-PE40 to define the role of sequences in domains II, Ib, and III. Various mutations were made in these domains and mutant forms of TGF alpha-PE40 expressed in Escherichia coli. Mutant proteins were then tested for their ADP-ribosylation, EGF receptor-binding, and cell-killing activities. Additionally, the amino boundary of domain III, which contains the ADP-ribosylation activity, was determined by deletion analysis. Data indicate that (i) the functional amino terminus of domain III is near amino acid 400; (ii) deletion of various regions in domain II or conversion of cysteines 265 and 268 to serines results in a loss of cytotoxicity which ranged from 10-fold to more than 150-fold, indicating that domain II is essential for full expression of cytotoxicity; (iii) deletion of the amino terminus of domain Ib results in a molecule with somewhat increased cytotoxic activity, indicating that domain Ib is not essential for the cytotoxic effect of TGF alpha-PE40; and (iv) TGF alpha-PE40, produced by denaturing and refolding of insoluble material from inclusion bodies, binds better to EGF receptors and is about 10-fold more cytotoxic to cells bearing EGF receptors than is the secreted form of soluble TGF alpha-PE40.