gebhart/patrepeval huggingface dataset:
Mechanism of Glibenclamide Inhibition of Cystic Fibrosis Transmembrane Conductance Regulator Cl− Channels Expressed in a Murine Cell Line (1997)

1. The sulphonylurea drug glibenclamide is a widely used inhibitor of the cystic fibrosis transmembrane conductance regulator (CFTR). To investigate how glibenclamide inhibits CFTR, we studied CFTR Cl- channels using excised inside-out membrane patches from cells expressing wild-type human CFTR. 2. Addition of glibenclamide (10-100 microM) to the intracellular solution caused a concentration-dependent decrease in the open time of CFTR Cl- channels, but closed times did not change. This suggests that glibenclamide is an open-channel blocker of CFTR. 3. Glibenclamide is a weak organic acid. Acidification of the intracellular solution relieved glibenclamide inhibition of CFTR, suggesting that the anionic form of glibenclamide inhibits CFTR. 4. To begin to identify the glibenclamide binding site in CFTR, we investigated whether glibenclamide competes with either MgATP or Cl- ions for a common binding site. Glibenclamide inhibition of CFTR was unaffected by nucleotide-dependent stimulation of CFTR, suggesting that glibenclamide and intracellular MgATP interact with CFTR at distinct sites. 5. Glibenclamide inhibition of CFTR was voltage dependent and enhanced when the external Cl- concentration was decreased. The data suggest that glibenclamide and Cl- ions may compete for a common binding site located within a large intracellular vestibule that is part of the CFTR pore.
Monoclonal Antibodies in the Diagnosis and Treatment of B-Cell Lymphomas (1991)

"Monoclonal Antibodies in the Diagnosis and Treatment of B-Cell Lymphomas." Baylor University Medical Center Proceedings, 4(4), pp. 27–28
Regulation of the alginate biosynthesis gene algC in Pseudomonas aeruginosa during biofilm development in continuous culture (1995)

Reporter gene technology was used to observe the regulation of the alginate biosynthesis gene, algC in a mucoid strain of Pseudomonas aeruginosa in developing and mature biofilms in continuous culture on Teflon and glass substrata. The plasmid pNZ63, carrying an algC-lacZ transcriptional fusion, was shown to not be diluted in continuous culture over a period of 25 days in the absence of selection pressure. Biofilm cells under bulk phase steady-state conditions demonstrated fluctuations in algC expression over a 16-day period, but no trend of increased or decreased expression over the time interval was indicated. In vivo detection of algC up-expression in developing biofilms was performed with a fluorogenic substrate for the plasmid-borne lacZ gene product (beta-galactosidase) by using microscopy coupled with image analysis. By this technique, cells were tracked over time and analyzed for algC activity. During the initial stages of biofilm development, cells already attached to a glass surface for at least 15 min exhibited up-expression of algC, detectable as the development of whole-cell fluorescence. However, initial cell attachment to the substratum appeared to be independent of algC promoter activity. Furthermore, cells not exhibiting algC up-expression were shown to be less capable of remaining at a glass surface under flowing conditions than were cells in which algC up-expression was detected.
Stimulation of megakaryocytopoiesis by acute thrombocytopenia in rats (1976)

Rats were made acutely thrombocytopenic by injection of antiplatelet serum. Marrow sections and squash preparations were made at intervals during 120 hr. Determinations were made of mitotic index, stage of maturation, ploidy level, and cell size of megakaryocytes; number and size of platelets were measured. Increased endomitosis among megakaryocytes was followed by an increase in the proportion of immature megakaryocytes, a greater average ploidy level of recognized megakaryocytes, and larger megakaryocytes. Maximum changes in these several parameters occurred between 32 and 72 hr after induction of thrombocytopenia. By 120 hr all megakarocyte parameters were near normal. For about 3 days, beginning at about 36 hr, platelet numbers increased rapidly. Average platelet size rose and returned to normal within about 60 hr. Changes in ploidy and size of megakaryocytes were measured in the immature and mature maturation stages. The results suggest that the initial stimulus in response to acute thrombocytopenia acts primarily on diploid precursors, programming them to mature into a population of megakaryocytes with an average ploidy approximately one level greater than in normal rats and a proportionate increase in cell size. The larger megakaryocytes presumably produce more platelets, accounting for a major part of the increased rate of platelet production. Since the changes in megakaryocytes begin to reverse before circulating platelet numbers have reached the normal level, reversal of the stimulus appears to be initiated by some change other than platelet mass.
Analysis of thyroglobulin iodination by tandem mass spectrometry using immonium ions of monoiodo‐ and diiodo‐tyrosine (2005)

Peptides containing a monoiodo- or diiodo-tyrosine residue (monoiodo-Y, diiodo-Y) were found to generate abundant immonium ions following collision-induced dissociation at m/z 261.97 and 387.87 Da, respectively. These residue-specific marker ions are between about 140 mDa (monoiodo-Y) and 300 mDa (diiodo-Y) mass deficient relative to any other peptide fragment ions of unmodified peptides, qualifying them as highly specific marker ions for tyrosine iodination when analyzed by high resolution tandem mass spectrometry (MS/MS). Two new iodination sites (Y-364 and Y-2165) were pinpointed in bovine thyroglobulin by MS/MS using these iodotyrosine-specific marker ions and combined tryptic/chymotryptic digestion.
Infrared Quantum Dots (2005)

Abstract Colloidal nanocrystals are quantum‐size‐effect tunable; offer an abundance of available surface area for electronic and chemical interactions; and are processible from organic or aqueous solution onto substrates rigid or flexible, smooth or rough, flat or curved, inorganic or organic (including biological), crystalline or amorphous, conducting, semiconducting, or insulating. With the benefit of over a decade's progress in visible‐light‐emitting colloidal‐quantum‐dot synthesis, physical chemistry, and devices, significant progress has recently been made in infrared‐active colloidal quantum dots and devices. This progress report summarizes the state‐of‐the‐art in infrared colloidal quantum dots, with an emphasis on applications and devices. The applications of interest surveyed include monolithic integration of fiber‐optic and free‐space‐communications photonic components with electronic substrates such as silicon and glass; in‐vivo biological tagging in infrared spectral bands in which living tissue is optically penetrable to a depth of 5–10 cm; solar and thermal photovoltaics for energy conversion; and infrared sensing and imaging based on non‐visible, including thermal, signatures. The synthesis and properties of quantum dots are first reviewed: photoluminescence quantum efficiencies greater than 50 % are achievable in solution, and stable luminescent dots are available in organic and aqueous solvents. Electroluminescent devices based on solution processing have been reported with external quantum efficiencies approaching 1 %. Photoconductive devices have been realized with 3 % internal quantum efficiencies, and a photovoltaic effect was recently observed. Electro‐optic modulation achieved by either field‐ or charge‐induced modification of the rate of optical absorption has been demonstrated based both on interband and intersubband (intraband) transitions. Optical gain from these processible materials with a threshold of 1 mJ cm –2 and an optical net modal gain coefficient of 260 ± 20 cm –1 have been reported.
Advanced robotics: redundancy and optimization (1991)

Advanced robotics: redundancy and optimization , Advanced robotics: redundancy and optimization , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Neutrophils Can Adhere Via α4β1 -Integrin Under Flow Conditions (1997)

Abstract In this study we investigated the possibility that an alternative pathway exists for neutrophil recruitment, namely an α4β1 -dependent pathway. A parallel plate chamber was used to investigate whether neutrophils could tether, roll, and adhere to tumor necrosis factor α (TNFα)-stimulated endothelium via α4β1 . α4β1 -integrin was induced on neutrophils using dihydrocytochalasin B and either an endogenous (endothelial-derived) chemotactic agent or an exogenous chemotactic molecule. α4β1 -expressing neutrophils could stably adhere under shear force (2 dyne/cm2) to TNFα-stimulated endothelium independent of the β2 -integrin. The firm adhesion was entirely abolished by antibodies directed against either the α4 or β1 -integrin subunits. However, the rolling interaction was not dependent on α4β1 but was abolished by antiselectin therapy. Neutrophils expressing α4β1 could also tether to the endothelium in the presence of antiselectin therapy, but at shear stresses less than 2 dyne/cm2. α4β1 -expressing neutrophils also tethered to and stably adhered (no rolling) to VCAM-1– but not to ICAM-1–transfected L cells. The interaction only occurred at shear stress less than 2 dyne/cm2. A cell line (Ramos) known to express high quantities of α4β1 -integrin interacted with VCAM-1–transfected L cells at very similar shear conditions. α4β1 -expressing neutrophils were also able to adhere to a second α4 -integrin ligand, fibronectin; however, this interaction only occurred under static conditions. These data suggest that, under certain conditions, neutrophils can adhere independently of the β2 -integrin pathway and adhere via the α4β1 -integrin. This study refutes the concept that α4β1 -integrin adhesion is restricted to mononuclear leukocytes and is not functional on human neutrophils.
Mining Textual Answers with Knowledge-Based Indicators (2000)

This paper describes a knowledge-based methodology of mining textual answers into large collections of texts. We present SOMBRERO, a knowledge processing module implemented in the LASSO question answering system. The module bootstraps question taxonomies, used for the search and validation of answers. Answer evaluation is produced through an expandable set of abduction rules. Background When people use computer-based tools to nd answers to general questions, they often are faced with a daunting list of search results, or \\hits&amp;quot; returned by a search engine. To take a step closer to information retrieval rather than document retrieval, this year the Text REtrieval Conference (TREC) has initiated an experimental track: the Question/Answering (Q/A) track, whose aim is to foster research in the area of textual Q/A, especially when pursued in a domain independent manner. The TREC Q/A Track species two restrictions for the questions. First, questions should have an exact answer tha...
Arteriogenesis The Development and Growth of Collateral Arteries (2003)

In patients with atherosclerotic vascular diseases, collateral vessels bypassing major arterial obstructions have frequently been observed. This may explain why some patients remain without symptoms or signs of ischemia. The term "arteriogenesis" was introduced to differentiate the formation of collateral arteries from angiogenesis, which mainly occurs in the ischemic, collateral flow-dependent tissue. Many observations in various animal models and humans support that the remodeling of preexisting collateral vessels is the mechanism of collateral artery formation. This remodeling process seems to be mainly flow-mediated. It involves endothelial cell activation, basal membrane degradation, leukocyte invasion, proliferation of vascular cells, neointima formation (in most species studied), and changes of the extracellular matrix. The contribution of ischemia to arteriogenesis is still unclear, but arteriogenesis clearly can occur in the absence of any significant ischemia. It is questionable, whether collateral arteries also form de novo in ischemic vascular diseases. A better understanding of the mechanisms of arteriogenesis will be important for the design of more effective strategies for the treatment of patients with ischemic vascular diseases.
Weight Loss and Wasting Remain Common Complications in Individuals Infected with Human Immunodeficiency Virus in the Era of Highly Active Antiretroviral Therapy (2000)

It has been postulated that the use of highly active antiretroviral therapy (HAART) would reduce the occurrence of human immunodeficiency virus (HIV)-associated weight loss and wasting. To test this assumption, we evaluated, by means of longitudinal analysis, a prospective cohort of 469 HIV-infected individuals enrolled in a study of the impact of HIV on nutrition. Overall, 156 individuals in the cohort (33.5%) met at least 1 of these definitions of wasting. Furthermore, 58% of the cohort (289 patients) lost >1.5 kg of weight in a 6-month period between any 2 study visits. More than 50% of the cohort was receiving HAART at the time that they met 1 of the definitions of wasting; with regard to the occurrence of wasting; no differences were related to therapy.
Solution Structure of Eotaxin, a Chemokine That Selectively Recruits Eosinophils in Allergic Inflammation (1998)

The solution structure of the CCR3-specific chemokine, eotaxin, has been determined by NMR spectroscopy. The quaternary structure of eotaxin was investigated by ultracentrifugation and NMR, and it was found to be in equilibrium between monomer and dimer under a wide range of conditions. At pH </= 5 and low ionic strength, eotaxin was found to be predominantly a monomer. The three-dimensional structure of the eotaxin monomer solved at pH 5.0 revealed that it has a typical chemokine fold, which includes a 3-stranded beta-sheet and an overlying alpha-helix. Except for the N-terminal residues (residues 1-8), the core of the protein is well defined. The eotaxin structure is compared with the chemokines regulated upon activation, normal T-cell expressed and secreted (RANTES) and monocyte chemoattractant protein-1 (MCP-1); eotaxin binds only CC chemokine receptor CCR3, whereas RANTES binds many receptors including CCR3, and MCP-1 binds a distinct receptor, CCR2. The RMSD of the eotaxin ensemble of structures with the RANTES average minimized monomeric subunit is 5.52 +/- 0.87 A over all backbone atoms and 1.14 +/- 0.09 A over backbone atoms of residues 11-28 and 34-65. The most important difference between the structures is in the N-terminal residues that are unstructured in eotaxin but structured in RANTES and MCP-1. Several residues in the loop region of RANTES show similar packing in eotaxin (residues 11-17). As the N-terminal and loop regions have been shown to be critical for receptor binding and signaling, this structure will be useful for determining the basis for CCR3 selectivity of the eotaxin.
WDM Transmission over 320 km EDFA-Amplified SSMF Using 30 Gb/s Return-to-Zero Optical Differential 8-Level Phase-Shift Keying (OD8PSK) (2005)

Fiber transmission of optical differential 8-level phase-shift keying (OD8PSK) signals is demonstrated for the first time. Co-polarized 8 WDM channels of 10 Giga-symbol/s or 30 Gb/s return-to-zero (RZ) OD8PSK signals with a channel spacing of 50 GHz were transmitted over 320 km of standard single mode fiber (SSMF) with an EDFA spacing of 80 km. The BER of the worst WDM channel after transmission of 320 km was 2.3x10-5.
Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis (2002)

The authors have developed a simple and highly efficient system for generating allelic exchanges in both fast- and slow-growing mycobacteria. In this procedure a gene of interest, disrupted by a selectable marker, is cloned into a conditionally replicating (temperature-sensitive) shuttle phasmid to generate a specialized transducing mycobacteriophage. The temperature-sensitive mutations in the mycobacteriophage genome permit replication at the permissive temperature of 30 degrees C but prevent replication at the non-permissive temperature of 37 degrees C. Transduction at a non-permissive temperature results in highly efficient delivery of the recombination substrate to virtually all cells in the recipient population. The deletion mutations in the targeted genes are marked with antibiotic-resistance genes that are flanked by gammadelta-res (resolvase recognition target) sites. The transductants which have undergone a homologous recombination event can be conveniently selected on antibiotic-containing media. To demonstrate the utility of this genetic system seven different targeted gene disruptions were generated in three substrains of Mycobacterium bovis BCG, three strains of Mycobacterium tuberculosis, and Mycobacterium smegmatis. Mutants in the lysA, nadBC, panC, panCD, leuCD, Rv3291c and Rv0867c genes or operons were isolated as antibiotic-resistant (and in some cases auxotrophic) transductants. Using a plasmid encoding the gammadelta-resolvase (tnpR), the resistance genes could be removed, generating unmarked deletion mutations. It is concluded from the high frequency of allelic exchange events observed in this study that specialized transduction is a very efficient technique for genetic manipulation of mycobacteria and is a method of choice for constructing isogenic strains of M. tuberculosis, BCG or M. smegmatis which differ by defined mutations.
Cardioprotection and Thrombolysis by Anistreplase in Anesthetized Dogs (1995)

Anistreplase is a thrombolytic agent comprising a complex of streptokinase, lys-plasminogen, and a p-anisoyl group, which temporarily protects the catalytic center of the enzyme complex. Streptokinase was previously shown to reduce infarct size (IS) in dogs with a fibrin-rich clot in the left anterior descending coronary artery (LAD) without necessarily producing reperfusion. Therefore, we hypothesized that IS in this model would be reduced by anistreplase. In addition, we studied the effect of tissue-type plasminogen activator (t-PA) on IS, testing our hypothesis in anesthetized dogs in which thrombin (100 U) and calcium (50 microliters, 0.05 M) were sequentially injected into the LAD to form a thrombus, anistreplase [0.01, 0.05, or 0.10 U/kg intravenous (i.v.) bolus], t-PA (0.1, 0.5, 2, or 8 micrograms/kg/min infusion for 60 min) or vehicle (VEH) was administered 55 min later. Anistreplase (0.05 or 0.10 U/kg) significantly (p < 0.05) reduced clot weight (VEH 22 +/- 3 mg; anistreplase 0.05 U/kg, 13 +/- 4 mg; anistreplase 0.10 U/kg, 0.7 +/- 0.6 mg), increased incidence of reperfusion (VEH 0%; anistreplase 0.05 U/kg, 42%; anistreplase 0.10 U/kg, 100%) and reduced IS (VEH 23 +/- 3%; anistreplase, 0.05 U/kg, 14 +/- 2%; anistreplase 0.10 U/kg, 15 +/- 2%). t-PA reduced thrombin weight (VEH 26 +/- 3 mg; 2 micrograms/kg/min t-PA 12 +/- 4; 8 micrograms/kg/min t-PA 2 +/- 2 mg) and increased incidence of reperfusion (VEH 0%; 2 micrograms/kg/min 75%; 8 micrograms/kg/min 100%), but IS was not altered (VEH 19 +/- 3%; 0.1 microgram/kg/min 18 +/- 3%; 0.5 microgram/kg/min 23 +/- 2%; 2 micrograms/kg/min 16 +/- 5%; 8 micrograms/kg/min: 19 +/- 3%).(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis and Reduction Kinetics of Sterically Shielded Pyrrolidine Nitroxides (2012)

A series of sterically shielded pyrrolidine nitroxides were synthesized, and their reduction by ascorbate (vitamin C) indicate that nitroxide 3, a tetraethyl derivative of 3-carboxy-PROXYL, is reduced at the slowest rate among known nitroxides, i.e., at a 60-fold slower rate than that for 3-carboxy-PROXYL.
Real-Time Observation of Organic Cation Reorientation in Methylammonium Lead Iodide Perovskites (2015)

The introduction of a mobile and polarized organic moiety as a cation in 3D lead-iodide perovskites brings fascinating optoelectronic properties to these materials. The extent and the time scales of the orientational mobility of the organic cation and the molecular mechanism behind its motion remain unclear, with different experimental and computational approaches providing very different qualitative and quantitative description of the molecular dynamics. Here we use ultrafast 2D vibrational spectroscopy of methylammonium (MA) lead iodide to directly resolve the rotation of the organic cations within the MAPbI3 lattice. Our results reveal two characteristic time constants of motion. Using ab initio molecular dynamics simulations, we identify these as a fast (∼300 fs) "wobbling-in-a-cone" motion around the crystal axis and a relatively slow (∼3 ps) jump-like reorientation of the molecular dipole with respect to the iodide lattice. The observed dynamics are essential for understanding the electronic properties of perovskite materials.
A Short Sequence in the p60src N Terminus Is Required for p60src Myristylation and Membrane Association and for Cell Transformation (1984)

We have constructed mutants by using linker insertion followed by deletion in the region of cloned Rous sarcoma virus DNA coding for the N-terminal 9 kilodaltons of the src protein. Previous work implicated this region in the membrane association of the protein. The mutations had little effect on src tyrosine kinase activity. Substitution of a tri- or tetrapeptide for amino acids 15 to 27, 15 to 49, or 15 to 81 had little effect on the in vitro transforming capacity of the virus. Like wild-type p60src, the src proteins of these mutants associated with plasma membranes and were labeled with [3H]myristic acid. In contrast, a mutant whose src protein had the dipeptide Asp-Leu substituted for amino acids 2 to 81 and a mutant with the tripeptide Asp-Leu-Gly substituted for amino acids 2 to 15 were transformation defective, and the mutant proteins did not associate with membranes and were not labeled with [3H]myristic acid. These results suggest that amino acids 2 to 15 serve as an attachment site for myristic acid and as a membrane anchor. Since deletions including this region prevent transformation, and since tyrosine kinase activity is not diminished by the deletions, these results imply that target recognition is impaired by mutations altering the very N terminus, perhaps through their effect on membrane association.
Detection of Single-Molecule DNA Hybridization Using Enzymatic Amplification in an Array of Femtoliter-Sized Reaction Vessels (2008)

Improving the sensitivity of DNA biosensors is extremely important in clinical diagnostics, gene therapy, and a variety of other biomedical studies. In this regard, we have developed a highly sensitive single molecule DNA assay platform with a 1fM experimental detection limit using enzymatic amplification in an array of femtoliter-sized reaction wells. To validate the utility of this technology in our study, we employed a fiber optic array to create thousands of femtoliter-sized reaction wells, each specifically functionalized with oligonucleotide probes capable of capturing biotinylated target DNA. After hybridization, the fiber was incubated with streptavidin-labeled enzyme solution. The bound single enzyme molecules were confined to individual reaction vessels containing excess fluorogenic substrate and catalyzed the production of a sufficient number of fluorescent product molecules to generate a detectable signal. At low target DNA concentrations with relatively short incubation times, only a small percentage of the capture sites bind target DNA, enabling a binary readout of target concentration from the high-density fiber array. This simple binary readout-based scheme is easy to perform and exhibits a high signal-to-noise ratio in the presence of trace amounts of DNA target. Furthermore, it also should be possible to extend this technology to protein detection by modifying the reaction wells with specific capture antibodies. We expect this assay to be useful in a number of biomedical applications where accurate and highly sensitive target analysis is critical.