gebhart/patrepeval huggingface dataset:
Negative Enrichment of Target Cells by Microfluidic Affinity Chromatography (2011)

A three-dimensional microfluidic channel was developed for high-purity cell separations. This system featured high capture affinity using multiple vertical inlets to an affinity surface. In cell separations, positive selection (capture of the target cell) is usually employed. Negative enrichment, the capture of nontarget cells and elution of target cells, has distinct advantages over positive selection. In negative enrichment, target cells are not labeled and are not subjected to strenuous elution conditions or dilution. As a result, negative enrichment systems are amenable to multistep processes in microfluidic systems. In previous work (Li, P.; Tian, Y.; Pappas, D. Anal. Chem.2011, 83, 774-781), we reported cell capture enhancement effects at vertical inlets to the affinity surface. In this study, we designed a chip that has multiple vertical and horizontal channels, forming a three-dimensional separation system. Enrichment of target cells showed separation purities of 92-96%, compared with straight-channel systems (77% purity). A parallelized chip was also developed for increased sample throughput. A two-channel system showed similar separation purity with twice the sample flow rate. This microfluidic system, featuring high separation purity and ease of fabrication and use is suitable for cell separations when subsequent analysis of target cells is required.
Evolution of object-relational database technology in DB2 (2002)

The paper defines the object-relational approach to database management and examines its advantages. It summarizes the features that are expected in an object-relational system, and discusses how these features are influencing the ANSI/ISO SQL Standard. Using DB2 as an example, it describes how object-relational features can be used to meet the needs of advanced database applications.
Long-term physiological effects of enhanced O2 release by inositol hexaphosphate-loaded erythrocytes. (1987)

A continuous lysing and resealing procedure with erythrocytes permitted incorporation in these cells of inositol hexaphosphate (InsP6), a strong allosteric effector of Hb. This leads to significant rightward shifts of the HbO2 dissociation curves with in vitro P50 (partial pressure of O2 at 50% Hb saturation), values increasing from 32.2 +/- 1.8 torr for control erythrocytes to 86 +/- 60 torr (pH 7.40; PCO2 40 torr at 37 degrees C; 1 torr = 1.333 X 10(2) Pa). The shape of the dissociation curve was still sigmoidal, although the Hill coefficient was decreased. The life span of InsP6-loaded erythrocytes equaled that of control erythrocytes. The long-term physiological effects of the InsP6-loaded erythrocytes on piglets were increased O2 release and reduced cardiac output. The reduced O2 affinity of the InsP6-loaded erythrocytes was still effective 20 days after transfusion in awake piglets. The electrolyte concentration appeared stable over the 5-day observation period except for a transient, but significant, hyperkalemia immediately after transfusion. The reductions in the O2 affinity of Hb reported here are large compared with previously reported values. Introduction of InsP6 into viable erythrocytes improves tissue oxygenation when, for any reason, normal blood flow is impaired.
Identification of Inhibitor Specificity Determinants in a Mammalian Phosphodiesterase (1999)

Mammalian phosphodiesterase types 3 and 4 (PDE3 and PDE4) hydrolyze cAMP and are essential for the regulation of this intracellular second messenger in many cell types. Whereas these enzymes share structural and biochemical similarities, each can be distinguished by its sensitivity to isozyme-specific inhibitors. By using a series of chimeric enzymes, we have localized the region of PDE4 that confers sensitivity to selective inhibitors. This inhibitor specificity domain lies within a short sequence at the carboxyl terminus of the catalytic domain of the protein, consistent with the competitive nature of inhibition by these compounds. Surprisingly, the identified region also includes some of the most highly conserved residues among PDE isoforms. A yeast-based expression system was used for the isolation and characterization of mutations within this area that confer resistance to the PDE4-specific inhibitor rolipram. Analysis of these mutants indicated that both conserved and unique residues are required for isoform-specific inhibitor sensitivity. In some cases, combined point mutations contribute synergistically to the reduction of sensitivity (suppression of IC50). We also report that several mutations display differential sensitivity changes with respect to distinct structural classes of inhibitors.
Phylogenetic conservation of cysteine proteinases. Cloning and expression of a cDNA coding for human cathepsin S. (1992)

A 1.8-kilobase full-length cDNA of human cathepsin S, a lysosomal cysteine proteinase, has been isolated. The single long open reading frame encodes a polypeptide of 331 amino acids consisting of a 15-amino acid NH2-terminal signal peptide, a propeptide of 99 amino acids, and a mature polypeptide of 217 amino acids. The deduced amino acid sequence contains only one potential N-glycosylation site located in the propeptide. The NH2-terminal amino acid sequence of the mature polypeptide was confirmed by sequencing cathepsin S purified from human spleen. The cDNA detects a 1.9-kilobase transcript in poly(A)+ RNA from human fibroblasts. Expression of human cathepsin S in transfected baby hamster kidney cells resulted in up to more than 300-fold cathepsin S activity as compared to untransfected controls. In the expressing baby hamster kidney cells, human cathepsin S is transported to the lysosomes via the mannose 6-phosphate receptor pathway as shown by density gradient centrifugation, immunofluorescence, and detection of the 37-kDa cathepsin S precursor in the medium in the presence of NH4Cl. The deduced amino acid sequence of human cathepsin S exhibits a substantial degree of similarity with other human cysteine proteinases and papain indicating that they have a common ancestral gene and are members of a gene family.
Intracellular transport of class I MHC molecules in antigen processing mutant cell lines. (1993)

Intracellular transport and stability of class I MHC glycoproteins depends on the assembly of H chain, beta 2-microglobulin, and peptide. The Ag processing mutant cell lines T2 and RMA-S have defects in peptide loading of class I, resulting in reduced cell surface expression of class I molecules. Expression of class I molecules in the murine cell line RMA-S can be induced at 26 degrees C, suggesting that they are transported to the cell surface, but are unstable. However, most human class I molecules in T2 are poorly expressed at the cell surface, even at 26 degrees C. To directly compare the transport of human and mouse alleles in RMA-S and T2, the human alleles HLA-A2, A3, and B27 were transfected into RMA-S along with human beta 2-microglobulin, and the mouse alleles H-2Kb and Db were transfected into T2. Surface expression of HLA-A3 and B27 in RMA-S remained less than 10% of wild-type levels at 26 degrees C. H-2Kb and Db in both cell lines, however, were expressed at 20 to 30% wild-type levels at 37 degrees C and could be induced to wild-type levels at 26 degrees C or with peptides. The selective expression of murine class I glycoproteins at the cell surface of T2 is not because of their greater stability when associated with human beta 2m, since H-2Kb and Db H chain/human beta 2m complexes dissociate more rapidly in vitro than HLA-A3 and B27 complexes. These results suggest that the difference in transport between human and mouse class I in T2 reflects a fundamental structural property of the class I glycoproteins.
Frustration in protein–DNA binding influences conformational switching and target search kinetics (2011)

Rapid recognition of DNA target sites involves facilitated diffusion through which alternative sites are searched on genomic DNA. A key mechanism facilitating the localization of the target by a DNA-binding protein (DBP) is one-dimensional diffusion (sliding) in which electrostatic forces attract the protein to the DNA. As the protein reaches its target DNA site, it switches from purely electrostatic binding to a specific set of interactions with the DNA bases that also involves hydrogen bonding and van der Waals forces. High overlap between the DBP patches used for nonspecific and specific interactions with DNA may enable an immediate transition between the two binding modes following target site localization. By contrast, an imperfect overlap may result in greater frustration between the two potentially competing binding modes and consequently slower switching between them. A structural analysis of 125 DBPs indicates frustration between the two binding modes that results in a large difference between the orientations of the protein to the DNA when it slides compared to when it specifically interacts with DNA. Coarse-grained molecular dynamics simulations of in silico designed peptides comprising the full range of frustrations between the two interfaces show slower transition from nonspecific to specific DNA binding as the overlap between the patches involved in the two binding modes decreases. The complex search kinetics may regulate the search by eliminating trapping of the protein in semispecific sites while sliding.
Synthesis of Azolyl Carboximidamides as Ligands for Zn(II) and Cu(II):  Application of the Zn(II) Complexes as Catalysts for the Copolymerization of Carbon Dioxide and Epoxides1 (2006)

A series of novel S,N-heterocyclic (thiazolyl) substituted carboximidamides 3 and 4 was synthesized in yields up to 82% from specific triazinium salts 1 and primary or secondary amines 2 which additionally bear pyridine or imidazole units. These carboximidamides are used as tailor-made ligands for the complexation of Cu(II) and Zn(II). The coordination behavior of 3 and 4 and the properties of the resulting metal complexes are affected a significant extent especially by the nature of these amine substituents. The most important structural feature of the novel complexes is that the ligation of the metal cations is achieved by a 1,3,5-triazapentadienyl anion system, compare the X-ray structure of the model complex Cu-4d. Analogous Zn(II) complexes 5, 6a, 6b, 6c, 7a, and 7b were obtained from carboximidamides 3, 4a, 4b, 4c, 4d, and 4e after reaction with diethylzinc. Interestingly, these Zn(II) complexes possess an intrinsic activity to catalyze the copolymerization of cyclohexene oxide and carbon dioxide to give polycarbonates 15 (TON up to 113; Turn Over Number: moles of substrate 14 consumed per moles of zinc. Molecular weights: up to 206.10(3) Da). Contaminations of 15 by polyethers are produced only in remarkably small amounts.
Requirement-based data cube schema design (1999)

On-line analytical processing (OLAP) requires efficient processing of complex decision support queries over very large databases. It is well accepted that pre-computed data cubes can help reduce the response time of such queries dramatically. A very important design issue of an efficient OLAP system is therefore the choice of the right data cubes to materialize. We call this problem the data cube schema design problem. In this paper we show that the problem of finding an optimal data cube schema for an OLAP system with limited memory is NP-hard. As a more computationally efficient alternative, we propose a greedy approximation algorithm cMP and its variants. Algorithm cMP consists of two phases. In the first phase, an initial schema consisting of all the cubes required to efficiently answer the user queries is formed. In the second phase, cubes in the initial schema are selectively merged to satisfy the memory constraint. We show that cMP is very effective in pruning the search space for an optimal schema. This leads to a highly efficient algorithm. We report the efficiency and the effectiveness of cMP via an empirical study using the TPC-D benchmark. Our results show that the data cube schemas generated by cMP enable very efficient OLAP query processing.
Synthesis of N-(2-phosphonylmethoxyethyl) derivatives of heterocyclic bases (1989)

The preparation of N-(2-phosphonylmethoxyethyl) derivatives of purine and pyrimidine bases, IV , as analogs of the antiviral 9-(2-phosphonylmethoxyethyl)adenine (PMEA, I ), is described. The synthesis consists in alkylation of alkali metal salts of heterocyclic bases or their N- or O-substituted derivatives with diethyl 2- p -toluenesulfonyloxyethoxymethylphosphonate ( IIa ), 2-chloroethoxymethylphosphonate ( IIb ) or 2-bromoethoxymethylphosphonate ( IIc ). The obtained N-(2-diethoxyphosphonylmethoxyethyl) derivatives of heterocyclic bases ( III ) were treated with bromotrimethylsilane to give phosphonic acids IV . Compounds IV were prepared from pyrimidines (uracil, cytosine and their 5-methyl derivatives), purines (adenine and its N 6 - and C(2)-substituted derivatives, hypoxanthine, guanine, 6-hydrazinopurine and 6-methylthiopurine etc.) and their analogs (3-deazaadenine etc.).
Yersiniatype III secretion (2002)

Pathogenic Yersinia spp (Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica) have evolved an exquisite method for delivering powerful effectors into cells of the host immune system where they inhibit signaling cascades and block the cells' response to infection. Understanding the molecular mechanisms of this system has provided insight into the processes of phagocytosis and inflammation.
WebIN-an architecture for fast deployment of IN-based personal services (2002)

The article outlines a hybrid architecture which subsumes IN services and can provide a realisation of merged content and communication services. It will substantially ease the manageability, scalability and distribution problems faced by IN solutions today. Furthermore, the architecture allows easier service creation, deployment and integration with system management for some enhanced IN services.
Efficient Depth‐of‐Field Rendering with Adaptive Sampling and Multiscale Reconstruction (2011)

Abstract Depth‐of‐field is one of the most crucial rendering effects for synthesizing photorealistic images. Unfortunately, this effect is also extremely costly. It can take hundreds to thousands of samples to achieve noise‐free results using Monte Carlo integration. This paper introduces an efficient adaptive depth‐of‐field rendering algorithm that achieves noise‐free results using significantly fewer samples. Our algorithm consists of two main phases: adaptive sampling and image reconstruction. In the adaptive sampling phase, the adaptive sample density is determined by a ‘blur‐size’ map and ‘pixel‐variance’ map computed in the initialization. In the image reconstruction phase, based on the blur‐size map, we use a novel multiscale reconstruction filter to dramatically reduce the noise in the defocused areas where the sampled radiance has high variance. Because of the efficiency of this new filter, only a few samples are required. With the combination of the adaptive sampler and the multiscale filter, our algorithm renders near‐reference quality depth‐of‐field images with significantly fewer samples than previous techniques.
Quantitative in vivo microdialysis study on the influence of multidrug transporters on the blood-brain barrier passage of oxcarbazepine: concomitant use of hippocampal monoamines as pharmacodynamic markers for the anticonvulsant activity. (2006)

Various antiepileptic drugs were shown to be substrates for multidrug transporters at the level of the blood-brain barrier. These ATP-dependent efflux pumps actively limit brain accumulation of xenobiotics and drugs. Intrahippocampal oxcarbazepine perfusion in rat was previously shown to exert anticonvulsant effects associated with increases in extracellular dopamine and serotonin levels. In contrast, preliminary studies in our laboratory revealed that no anticonvulsant or monoaminergic effects could be obtained after systemic oxcarbazepine administration. The present in vivo microdialysis study was conducted to investigate the impact of the transport kinetics of oxcarbazepine across the blood-brain barrier on the observed treatment refractoriness. More precisely, the influence of intrahippocampal perfusion of verapamil, a P-glycoprotein inhibitor, and probenecid, a multidrug resistance protein inhibitor, on the blood-brain barrier passage and anticonvulsant properties of oxcarbazepine were investigated in the focal pilocarpine model for limbic seizures. Simultaneously, the effects on hippocampal monoamines were studied as pharmacodynamic markers for the anticonvulsant activity. Although systemic oxcarbazepine administration alone failed in preventing the animals from developing seizures, coadministration with verapamil or probenecid offered complete protection. Concomitantly, significant increases in extracellular hippocampal dopamine and serotonin levels were observed within our previously defined anticonvulsant monoamine range. The present data indicate that oxcarbazepine is a substrate for multidrug transporters at the blood-brain barrier. Coadministration with multidrug transporter inhibitors significantly potentiates the anticonvulsant activity of oxcarbazepine and offers opportunities for treatment of pharmacoresistant epilepsy.
Methodological Issues of Clinical Research with EGFR Inhibitors (2007)

The epidermal growth factor receptor (EGFR) signaling plays a key role in tumorigenesis and it has been considered an attractive target for novel antitumoral agents. Small-molecule tyrosine kinase inhibitors such as gefitinib and erlotinib have been approved for the treatment of advanced non-small-cell lung cancer (NSCLC) patients. However, the positive results obtained in early clinical trials with gefitinib were not confirmed in large phase 3 trials, testing the efficacy of this drug in combination with chemotherapy or as single agent. An advantage in overall survival has been observed with erlotinib as single agent in NSCLC, but not in combination with chemotherapy. Conversely, an additive effect has been observed with the combination of the monoclonal antibody cetuximab and irinotecan in heavily pretreated patients with irinotecan-refractory colorectal cancer. The combination of cetuximab and radiotherapy or chemotherapy has also shown efficacy in patients with squamous cancer cell of head and neck. However, the major limit in the development of these agents is the lack of validated predictive markers of response that might allow appropriate selection of patients. In this review, we will discuss the major issues in clinical development of such agents, focusing on the challenges in designing and conducting clinical trials with EGFR inhibitors. Keywords: EGFR, gefitinib, erlotinib, lapatinib, cetuximab, panitumumab
Dipole Orientation Distributions in Langmuir−Blodgett Films by Planar Waveguide Linear Dichroism and Fluorescence Anisotropy (1996)

A method to determine the orientation distribution of fluorescent molecules in a thin, substrate-supported film is described. Attenuated total reflection spectrometry on the surface of a planar waveguide is used to measure absorption LD, from which the mean dipole tilt angle in the film is obtained. Steady-state fluorescence anisotropy is measured in a total internal reflection geometry on a film supported on fused silica but prepared under otherwise identical conditions. The angular distribution about the mean can be recovered from the anisotropy measurement by modeling the distribution as a probability density that is specified by two adjustable parameters. The method was tested on Langmuir−Blodgett (LB) films of arachidic acid doped with the fluorescent amphiphiles DiI and BODIPY. In the DiI-doped films, the mean tilt angle was 75° from the surface normal. Assuming a Gaussian distribution, the standard deviation was 12°, indicating a high degree of macroscopic order. In the BODIPY-doped films the distribution was 59 ± 17°, which indicates a less ordered assembly. Larger angular distributions were calculated using a step function model. The results show that dipoles in the headgroup region of arachidic acid LB films are more ordered than dipoles in the alkyl chain region. The method should prove useful in studying relationships between assembly technique, structure, and function in two-dimensional molecular arrays.
Intact learning and memory in rats following treatment with the dual orexin receptor antagonist almorexant (2010)

Rats treated with almorexant are fully capable of spatial and avoidance learning.
Characterization of Site-specific N-Glycosylation (2008)

Even if a consensus sequence has been identified for a posttranslational modification, the presence of such a sequence motif only indicates the possibility, not the certainty that the modification actually occurs. Proteins can be glycosylated on certain amino acid side chains, and these modifications are designated as C-, N-, and O-glycosylation. C-mannosylation occurs on Trp residues within a relatively loosely defined consensus motif. N-glycosylated species are modified at Asn residues of Asn-Xxx-Ser/Thr/Cys sequons (where Xxx can be any amino acid except proline). N-linked oligosaccharides share a common core structure of GlcNAc<sub>2</sub>Man<sub>3</sub>. In addition, an enzyme, peptide N-glycosidase F (PNGase F), removes most of the common N-linked carbohydrates unaltered from proteins while hydrolyzing the originally glycosylated Asn residue to Asp. O-glycosylation occurs at Ser, Thr, and Tyr residues, usually in sequence stretches rich in hydroxy-amino acids. O-glycosylation lacks a common core structure. Mammalian proteins have been reported bearing O-linked N-acetylgalactosamine, fucose, glucose, xylose, mannose, and corresponding elongated structures, as well as N-acetylglucosamine. Chemical methods are used to liberate these oligosaccharides because no enzyme would remove all the different O-linked carbohydrates. Characterization of both N- and O-glycosylation is complicated by the fact that the same positions within a population of protein molecules may feature an array of different carbohydrate structures, or remain unmodified. This site-specific heterogeneity may vary by species and tissue, and may also be affected by physiological changes. For addressing site-specific carbohydrate heterogeneity mass spectrometry has become the method of choice. Reversed-phase HPLC directly coupled with electrospray ionization mass spectrometry (LC/ESI-MS/MS) offers the best solution. Using a mass spectrometer as online detector not only assures the analysis of every component eluting (mass mapping), but also at the same time diagnostic carbohydrate ions can be generated by collisional activation that permits the selective and specific detection of glycopeptides. In addition, ESI-compatible alternative MS/MS techniques, electron-capture and electron-transfer dissociation, aid glycopeptide identification as well as modification site assignments.
Evaluation of the Novel Myocardial Perfusion Positron-Emission Tomography Tracer 18 F-BMS-747158-02 (2009)

18F-BMS-747158-02 is a very attractive new PET perfusion tracer that allows quantitative assessment of regional myocardial perfusion over a wide flow range. The long half-life of 18F renders this tracer useful for clinical PET/CT applications in the workup of patients with suspected or proven coronary artery disease.